In the age of the internet, literature is consumed in unprecedented ways. Modern social movements often call upon those of the past through key quotes and references to influential literary works. Quotes can go viral, seen outside of their context by thousands of people and become associated with these movements or rediscovered by new communities. For instance, key figures in post-WWII literature such as author and civil rights activist James Baldwin have had their words re-immortalized within the context of contemporary movements such as Black Lives Matter. Baldwin’s era of literature was one of marked social change and evolution within the literary world that parallels our society today, making it significant to understand how quotes from this period can reappear and spread across social media. To analyze the reception of post-war literature on Twitter, we utilized a dataset of over 40 million tweets quoting or referencing James Baldwin, as well as similar datasets quoting four other influential authors of the time including David Foster Wallace and Kurt Vonnegut. We focused on the patterns of text reuse (i.e., the repetition of known quotes) in tweets from 2006-2023, examining key moments of reception and exploring the context of virality for key quotes. During this context-finding process, we also developed a novel method for conducting self-identified user demographic analysis. We implemented clustering algorithms on both tweets and user bios, supplemented the resulting clusters with manual merging processes, and experimented with various visualization strategies. Our results yielded clear quote usage patterns for certain demographic groups, demonstrating the efficacy of the novel demographic extraction method. These methods can be expanded for further demographic-focused social media research and help us understand how cultural movements evolve today.

Autosomal Dominant Alzheimer’s Disease (ADAD) can result from a pathogenic variant in the PSEN2 gene, which encodes an integral membrane protein called Presenilin 2. This variant has been shown to result in a harmful change in the balance of amyloid-β types in neurons, which has been hypothesized to increase risk of dementia. The diverse capabilities of Presenilin give reason to hypothesize that there may be other effects of the variant protein that are connected to ADAD pathogenesis. Reduced spine density, a feature of ADAD pathology, may be caused by overactivity of synaptic pruning. This activity is mediated by resident innate immune cells in the brain called microglia. We sought to explore the effects of PSEN2 variants on microglia-neuronal interactions via the assessment of synaptic pruning in a human induced pluripotent stem cell (hiPSC) derived in vitro model. We differentiated CVIA2 isogenic and PSEN2 N141I variant hiPSCs into both microglia and neurons. Utilizing a coculture of both wild-type neurons and microglia with the PSEN2 N141I variant, we performed immunocytochemistry for synaptic proteins Synapsin 1 and PSD95a. We then imaged the microglia and neurons using confocal microscopy. We assessed differences in synaptic pruning by quantifying immunofluorescent signal of Synapsin in microglia. Specifically, we looked at the colocalization of synaptic protein expression with signal from microglia-specific protein Iba1. We hypothesized that the variant microglia would contain a significantly different amount of signal for Synapsin compared to that of a control sample of wild-type microglia and neurons, implying a change to synaptic pruning function. If altered microglial synaptic pruning activity is shown to play a role in ADAD pathogenesis, targeting microglia could become a possible therapeutic treatment for patients.

Within the field of anesthesia, the process of arousal following general anesthesia is still little understood. Of particular concern is the way a state of pain can modulate arousal, with the nucleus accumbens (NAc) as a brain region of interest as it serves many functions including controlling mood, pain states, and reward motivation. This study investigates how NAc principal cells change their firing during arousal and are influenced by a pre-existing pain state. To assess this, we leverage the partial sciatic nerve ligation model of chronic neuropathic pain to examine the influence of pain state on arousal. We then test groups of mice in their behavioral responses, including open field test, von Frey, hot plate test, and the return of righting reflex as a measure of arousal from isoflurane anesthesia-induced unconsciousness. In some mice, we record 1-photon calcium-related population activity in the NAc to analyze neural activity during arousal from anesthesia. Our findings will serve to illuminate the underlying brain circuitry involved in arousal from anesthesia and the influence of pain state, which can help improve anesthesia recovery and may reveal non-opioid or endogenous mechanisms for pain relief.

Soluble peptides from the HIV-1 (Human Immunodeficiency Virus) envelope heptad repeat-2 domain, known as HIV fusion inhibitors, can inhibit viral entry by blocking formation of the gp41 6-helix bundle required for membrane fusion and infection. However, this treatment is unfeasible because it requires twice-daily subcutaneous injections with high risk and cost. The Lieber Lab is working to engineer hematopoietic stem and progenitor cells (HSPCs) to express HIV fusion inhibitors in vivo, potentially offering sustained protection against HIV. In my work I used SIVmac239 (Simian Immunodeficiency Virus) challenged Rhesus Macaques sera and developed viremia (from another study by Lieber lab). My goal was to test whether anti-gp41 antibodies from these animals cross-reacted with synthetic gp41-derived fusion inhibitor peptides, specifically C46-v2o, C34-SFT, and Enfuvirtide(T20). If antibodies interfered with fusion inhibitors, their therapeutic effect would be severely compromised. In my project, I developed an Enzyme-Linked Immunosorbent Assay (ELISA) to measure antibody titers. These peptides were coated, then blocked with 3% bovine serum albumin, and incubated with diluted Macaque serum to allow antibody binding. I used anti-monkey immunoglobulin-G conjugated with Horseradish Peroxidase for detection of antibody binding. I optimized the serum dilution to 1:200 to reduce background signal and concluded SIV-challenged Macaques had detectable antibody levels against C46-v2o and C34-SFT, but not T20. Ongoing work will determine more detailed IC50 antibody titers in serum samples. Notably, animals with high viral loads exhibited higher levels of antibodies against HIV fusion inhibitors. T20 is a promising candidate for sustained HIV inhibition, as no detectable antibodies means it’s less susceptible to pre-existing immune responses. These findings provide valuable insights into how fusion inhibitors interact with the immune system and help refine strategies for HSPC-based HIV therapies, bringing us closer to a long-term, self-sustaining approach for HIV prevention. 
 

Autism Spectrum Disorders (ASD) are a combination of neurological and developmental abnormalities, with 1 in every 36 children diagnosed worldwide. Brain Selective Kinase 2 (BRSK2) is one of the strongest autism-associated genes, with 35 de novo mutations reported to date. Patients harboring BRSK2 variants clinically present with neurodevelopmental disorders, including speech delay, intellectual disability, motor dysfunction, and behavioral abnormalities. Despite its strong ASD association, the molecular functions of BRSK2 and the mechanisms through which it regulates neurodevelopment remain unclear. My project aims to investigate the molecular role of BRSK2 by identifying its localization in the developing hippocampal and cortical neurons. The function of a gene is reliant upon its localization within the cell. To identify the subcellular localization of BRSK2 during early neurodevelopment, I am analyzing the subcellular distribution of BRSK2 in cultured primary embryonic rat neurons at different developmental time points, using immunocytochemistry and confocal microscopy. To delineate the impact of missense mutations in BRSK2 on its localization, I am analyzing the phenotype of cultured hippocampal rat neurons with GFP-tagged engineered constructs harboring the BRSK2 mutants. My analysis found that both hippocampal and cortical neurons display mostly cytoplasmic BRSK2 localization, with a significant association with the subcellular endomembrane as well as the plasma membrane (PM). Interestingly, BRSK2 was also found at the dendritic spines at day in vitro (DIV) 12. We are currently investigating whether any of these missense mutations disrupt inter-organelle communication between the endomembranes and plasma membrane. BRSK2’s localization in the endomembranes could explain disruptions in protein processing, dendritic development, or neuronal polarity linked with the missense mutations that eventually impact neurodevelopment, leading to autism. Discovering BRSK2’s localization will help contribute toward the future development of targeted therapies for ASD caused by the dysfunction of the BRSK2 kinase.

Prenatal lead exposure is associated with learning and behavior problems, reduced growth, and increased risk of miscarriages. The Centers for Disease Control and Prevention and the American College of Obstetricians and Gynecologists recommend lead exposure screening for pregnant women due to the significant health risks lead poses to their developing fetus. However, there is no nationally recognized screening tool, leading to inconsistent practices and potential gaps in care across the country. This project aimed to address this gap by identifying state-specific screening resources for clinicians and creating a tool to help healthcare providers more easily access these resources. Through web searches, emails, and phone calls to 50 state health departments, 20 state-level screening resources were identified, along with county-level resources in three counties with childhood lead poisoning prevention programs. These resources were compiled into an interactive map directing clinicians to screening resources in their region. This tool is being reviewed for potential use by the Pediatric Environmental Health Specialty Units, an organization that provides free pediatric and reproductive environmental health consultation services to clinicians. The tool addresses the barrier to accessing screening resources, ideally increasing lead screening rates and improving pediatric health outcomes. The findings highlight the need for a national screening tool and provide insights into regional differences in recommended screening practices.

Microbial odors are essential for attracting mosquitoes to their hosts, but their role in attraction to other nutrient sources remains unknown. Sugar sources provide nutrients that lengthen the lifespan of both male and female mosquitoes and increase the vectorial capacity in host-seeking female mosquitoes. Microbial odors have been shown to act as proxy signals for the availability and composition of certain nutrients, such as amino acids and mineral ions, found in nectar and fruit sap. As microbes are abundant in flowers and fruits, we hypothesize that Microbial Volatile Organic Compounds (mVOCs) from these nutrient sources play an important role in the feeding behavior of mosquitos. To test this, we analyzed the microbial community of a known attractive fruit, Mangifera indica ‘Keitt.’ Microbial species were identified from our environmental samples through amplicon sequencing of the 16S and 26S regions. Isolates of the most abundant and relevant species were cultured for mVOC collection and chemical analysis via Gas Chromatography and Mass Spectroscopy (GC-MS). Behavioral assays were then performed with Aedes aegypti mosquitoes to observe the effect of microbial odors on the attractiveness of nutrient sources. Through the identification of behaviorally-relevant microbial compounds, we can gain a stronger understanding of the ecological dynamics of mosquito chemoreception and microbial community signaling, which can help inform future mosquito-control measures.

Orientation Patch Count (OPC) is a method of research used by biologists and paleontologists to analyze the complexity of an animal’s feeding surface while inferring their diets; diet and tooth complexity have evolved in concert with one another, which is why this method has been used on reptilian and mammalian (denticular) species. However, it has not been extensively tested on edentulous (toothless) clades. Therefore, my research examines the OPC of an edentulous species - specifically the endangered Madagascar big-headed turtle (Erymnochelys madagascariensis) using  three CT-scanned specimens. Three primary programs were used in order to analyze the quantitative morphometricsof the species: Slicer for processing and editing CT scans from the University of Washington’s Friday Harbor Lab, MeshLab for editing 3D models, and RStudio for data analysis. This research contributes to a broader study on turtle species led by paleontologist Brenlee Shipps, who will apply these findings to extinct beaked clades, specifically dicynodonts.

Dilated Cardiomyopathy (DCM) is a heart disease characterized by the thinning and dilation of the heart's walls, which leads to a decrease in blood pumping ability and can progress to heart failure. Many genetic mutations, primarily in components of the sarcomere, have been implicated in causing DCM. One such mutation is the beta myosin heavy chain mutation E525K. This project aims to understand the molecular mechanism by which E525K leads to disease progression using stem cell-derived cardiomyocytes and a unique multi-level approach to characterizing contractility and cell morphology. Here we show that the E525K mutation can lead to both hyper- and hypocontractility depending on the scale of the analysis. We found that in isolated cells, E525K mutants experienced a 65% decrease in sarcomere shortening and that in engineered heart tissues, the max force produced by tissues with mutant cells was 39% lower than WT tissues. Meanwhile, in isolated myofibrils with the mutation peak force was increased by 45% when stimulated with pCa 4.0 calcium. Morphological analysis showed that mutant cells on average have fewer, smaller, less organized sarcomeres than WT cells. This demonstrates that E525K myosin, though linked to DCM, which is associated with hypocontractility, exhibits both hyper- and hypocontractile effects. Cardiomyopathy affects an estimated 1 in 500 people worldwide and is a major cause of heart failure. Novel pharmacological treatments that activate or inhibit myosin are becoming available; however, cardiomyopathy’s genetic nature complicates treatment. Our findings highlight that the underlying mechanisms causing cardiomyopathy can vary greatly even between patients showing similar disease phenotypes. From a clinical perspective, this complicates what medications should be used, demonstrating that a deeper understanding of the underlying mechanism by which cardiomyopathy-related mutations cause disease is imperative to diagnose and treat patients optimally.

The Red-legged Honeycreeper, Cyanerpes cyaneus, is a member of the passerine bird family Thraupidae (tanagers) and is part of a group commonly called Neotropical honeycreepers.  Along with other honeycreeper species, C. cyaneus is a nectarivore, meaning that floral nectar is a large component of its diet.  It is expected that C. cyaneus, like other avian nectarivores, exhibits specialized adaptations to the tongue and bill and specialized feeding mechanisms for feeding on nectar, but this remains unexplored.  This study analyzes the kinematics (movements in space) of the bill and tongue during nectar feeding in C. cyaneus to investigate how this species is adapted for nectar feeding.  The feeding kinematics of C. cyaneus are then compared to those of three frugivorous (fruit-eating), but opportunistically nectarivorous, tanager species: the Crimson-backed tanager (Ramphocelus dimidiatus), the Palm tanager (Thraupis palmarum), and the Blue-grey tanager (Thraupis episcopus).  These opportunistic nectar feeders were given access to nectar and their feeding kinematics were characterized and compared to those of C. cyaneus to determine how ancestral patterns of feeding kinematics could be co-opted for specialized nectarivory.  Birds were filmed in Panama using high-speed videography and footage was digitized using the DLTdv8 imaging tool. Data were subsequently processed in Microsoft Excel and RStudio.  By comparing the feeding mechanics of C. cyaneus with those of closely related opportunistic nectarivores, this research aims to not only uncover the nectar extraction mechanisms used by C. cyaneus, but will be the first study to examine the evolutionary trajectory of nectar-feeding biomechanics.  These anticipated findings will contribute to a more comprehensive understanding of the evolution of avian nectarivory.

I investigate whether combining ultra-wideband (UWB) radar with inertial measurement units (IMUs) can produce more robust human pose estimations than using IMUs alone. UWB radar yields precise distance measurements, offering positional data that standard IMUs—sensitive mainly to angular velocity and acceleration—cannot capture. To test this approach, I built an embedded system that integrates a UWB radar module with wearable IMUs, then designed a user study involving everyday movements and targeted exercises performed by a small group of participants. This setup allowed me to collect a diverse dataset under realistic conditions. I processed these data using neural network models, including long short-term memory (LSTM) and transformer architectures, to generate accurate joint angles. I then fed those angles into a 3D skeleton reconstruction model. My preliminary findings suggest that the additional distance data from the UWB radar substantially improves tracking accuracy and reduces ambiguity in limb positioning. This enhanced estimation could lead to more realistic virtual reality avatars, improved fitness tracking, and better physical therapy tools. By overseeing the hardware design, data collection, and model development, I actively demonstrate how interdisciplinary methods can advance human-computer interaction through more precise and accessible pose estimation.

Soil-transmitted helminths impact over 1.5 billion people worldwide, disproportionately affecting school-aged children and pregnant women. Hosts issue a “weep and sweep” Type II immune response to expel helminth parasites from the intestines. Ruptured epithelial cells secrete the cytokine interleukin (IL)-33, which recruits innate lymphoid type 2 cells (ILCs)2 and CD4+ T-helper type 2 (Th2) cells. ILC2s release IL-13, encouraging stem cell differentiation into tuft and goblet cells to facilitate tissue repair and worm expulsion. Anemia is prevalent in helminth-rich environments because of elevated rates of malaria and malnutrition. Despite correlations between anemia and helminth infection, the impact of anemia on the Type II immune response in the small intestines remains unknown. Using N. brasiliensis (Nb), a bloodsucking hookworm-like parasite, I observed that one week post infection, iron-deficient (ID) mice were less capable of expelling worms compared to iron-sufficient (IS) mice. Through tuft cell immunofluorescence staining in the small intestine, I observed comparable hyperplasia in IS and ID-Nb infected mice but noticed differences in cell localization: ID-Nb infected mice had decreased numbers of tuft cells in the crypts compared to IS-Nb mice. This suggests that ID Nb-infected mice could be experiencing decreased migration/proliferation of tuft cells, compared to their IS-infected counterparts. Using EdU, a synthetic nucleotide tag that labels newly synthesized DNA, we can understand cellular proliferation patterns in IS vs. ID Nb mice. Co-staining for tuft cells permits us to merge events and track unique vs. universal trends in cell behavior, including cells’ migration patterns. I hypothesize that ID-Nb mice will have decreased cellular proliferation and migration compared to IS-Nb mice, ultimately impacting worm burden. These findings offer insights into the mechanism behind negative outcomes in anemic hosts, and could contribute to dietary intervention or therapies targeting the epithelium to alleviate burdens of helminth infection.

Circadian clocks have evolved as a powerful adaptation in response to daily environmental changes, allowing optimally timed sleep-wake cycles. The solar light-dark (LD) cycle is the dominant zeitgeber (time-giver) for entrainment (synchronization) of sleep and wake to external cues. While our lab has found that humans sleep less and later the days prior to the full moon phase where moonlight is available in the early night, moonlight was found to be an unreliable cue in determining lunar modulation of sleep for the light-polluted city population. Thus, my project investigates whether lunar cycling on activity patterns remains present without photic moonlight exposure using a diurnal non-human primate model: captive titi monkeys (Plecturocebus). The California National Primate Research Center collected titi monkey data (n=16) between 2022 to 2024 using AX3 from Axivity, a wearable data log that measures acceleration to monitor physical activity. I am using the statistical software R to derive activity onset and sleep onset/offset as phase markers of activity. Additionally, I am fitting different cosine models to a 30/15-day period, respectively lunar and semilunar, to analyze the periodic data for activity across the lunar month. We expect to see phase markers of activity oscillate with the monthly lunar phase, showing how the lunar cycle influences circadian rhythms in diurnal non-human primates, even in the absence of moonlight. This study may reveal a novel finding on lunar rhythms on activity patterns and could incur interest on how endogenous processes have adapted to the lunar cycle. Further molecular work could elucidate the neural mechanism behind lunar modulation of sleep and provide insights on improved treatment of dysregulated sleep.

Increased mitochondrial oxidative stress causes fatigue and metabolic dysfunction in muscle tissue. It is unclear whether the oxidative stress is due to elevated production or impaired consumption of reactive oxygen species (ROS). The purpose of this study is to test whether the capacity of the antioxidant defense system is impaired or the mitochondrial ROS production rate is elevated in response to chronic changes in mitochondrial oxidative stress. To experimentally manipulate mitochondrial oxidative stress, we use an inducible mouse model to knockdown superoxide dismutase 2 (SOD2) in skeletal muscle and heart to increase oxidative stress, and exercise training to decrease oxidative stress. Knockdowns (KD) or littermate controls (CON) performed a six-week voluntary wheel running (EX) or sedentary control intervention (SED). Following completion of the intervention, I isolated heart and skeletal muscle mitochondria using differential centrifugation. I measured mitochondrial hydrogen peroxide (H₂O₂) production rate and tested the antioxidant capacity by treating isolated mitochondria with Auranofin (AFN) or 1-chloro-2,4-dintrobenzene (CDNB), which inhibit the thioredoxin and glutathione S-transferase components of the mitochondrial antioxidant defense system, respectively. KD heart and skeletal muscle had similar absolute H₂O₂ production rates compared to CON, but normalized to oxygen consumption the KD had significantly higher H₂O₂ production. Since absolute H₂O₂ production under vehicle conditions was not different, this suggests that the antioxidant capacity adapts to meet the changes in mitochondrial H₂O₂ production. We will collect data from the exercise-trained cohort next month. I expect to see an increase in H₂O₂ production rate and antioxidant capacity in both groups due to the increased mitochondrial biogenesis from exercise training. These results demonstrate that chronic increases in mitochondrial oxidative stress decrease mitochondrial H₂O₂ production capacity from skeletal muscle.

4.5 million adults in the United States are diagnosed with chronic liver disease. Over time this can lead to cirrhosis, an end-stage condition in which scarring occurs in the liver. Reduced liver function from cirrhosis results in accumulations of neurotoxic substances that induce a spectrum of neurological impairments known as hepatic encephalopathy (HE). The critical flicker frequency (CFF) test is a well-established screening test for HE. Previously we developed Beacon, a novel and portable CFF measuring device that can be administered at home via smartphone app, as an accessible alternative to current CFF measurement devices that are large, expensive, and not intended for at-home use. We found that Beacon produced a CFF measurement that aligned with commercially available devices. While the current Beacon reflects current commercial devices, the efficiency of measurement is bottlenecked by the fact that pairs of flickering light stimuli can only be presented sequentially due to the singular light source. We therefore propose a dual headed version of Beacon that gives the option of flashing two frequencies simultaneously. I designed and developed a version of this dual-headed Beacon with sliding heads as well as an accompanying user interface before conducting a series of user studies, beginning with a pilot study on healthy individuals and progressing to a clinical trial on chronic liver disease patients, to evaluate the impact of the number of light sources and the distance between them on CFF measurement time and repeatability. I hypothesize that the two-headed Beacon will produce a CFF measurement more quickly than the original Beacon and that a closer distance between heads will also produce quicker and more consistent measurements. These findings will help inform the development of future iterations of the Beacon, leading to improved outcomes for chronic liver disease patients.

Intimate partner violence (IPV) is a widespread problem across the U.S. that typically begins in adolescence which can cause severe struggles for the impacted individuals. IPV can be mitigated through some preventative factors, such as education and understanding of IPV. The purpose of this study is to evaluate rejection sensitivity (RS)-- the tendency to strongly react to rejection, including the dismissal or refusal of ideas, people, or offers-- as a mediator between comprehensive sexuality education (CSE) and IPV. I designed this study to use a cross-sectional online survey to measure levels of RS, themes of CSE from middle and high school education, and levels of IPV that individuals have experienced. It includes a representative sample based on Unites States census data of 340 participants who range from 18-25 years and have had a romantic relationship lasting at least two months. The data is analyzed through a mediation model, with RS as the mediator, as well as testing the direct effects of CSE on IPV using R Statistical Software. Analysis models the three pathways: path a-- CSE to RS, path b-- RS to IPV, path C-- direct effects of CSE on IPV (CSE to IPV). I anticipate that RS will act as a mediator between CSE and IPV such that higher levels of CSE will be associated with lower IPV levels through the mediation of RS. Additionally, I hypothesize there will be a direct effect of CSE on IPV. This study aims to improve the understanding of potential preventative factors of IPV as well as inform future interventions, such as CSE. Keywords: intimate partner violence, rejection sensitivity, comprehensive sexuality education

This project investigates the effects of Chile’s 2020-2021 pension withdrawals on household consumption across food, housing, transportation, healthcare, and education. I use existing socio-economic household survey data for my analysis. Chile’s Covid response allowed civilians to withdraw up to 30% of their pensions, impacting 11 million workers and reducing pension assets by an estimated 22% of GDP. This policy mirrors actions in 30 other countries globally, now facing similar challenges. This research aims to address the literature gap in consumption research, and provide a framework for policymakers in affected nations to understand how the pension funds were used in terms of consumption. My role encompasses everything, from design to analysis. First, I make sure the two groups being compared (Chilean households who withdrew funds and who did not) were on similar spending paths before the withdrawals happened, known as pre-trend analysis. I use statistical tools, such as t-tests, to check if those trends were similar—basically confirming that the two groups were spending similarly before the policy change. Second, I use a statistical model, called Difference-in-Differences (DiD), to isolate the specific effect of the withdrawals from other things that might have affected spending. Third, I look at how the pension withdrawals affected retirees and non-retirees as well as different income demographics, to see if the impact was the same or different for everyone, known as heterogeneity analysis. As this project is in-progress, I assume I would find a statistically significant, varied impact on household consumption. I anticipate increased spending on essential purchases since the Covid crisis led to many financial difficulties that affected households' spending. These findings can help inform younger generations around the world about their decisions regarding their own retirement planning decisions, as this global issue disrupted their retirement savings.

Previous work has shown frequency-specific modulation of dorsal hippocampus (dHPC) neural activity during simple behavioral tasks, suggesting shifts in neural population activity during different task phases and animal behaviors. Relatively little is known about task-relevant orchestrated shifts in theta, beta, and gamma rhythms across multiple behavioral timescales during a complex task that requires repeatedly adapting behavioral strategies based on changing reward contingencies. To address this gap in knowledge, we used a spatial set-shifting task to determine whether dHPC plays a specific role in strategy switching. The task requires rats to use two spatial strategies on an elevated plus maze: 1) alternating between East and West reward locations or 2) always going to the same reward location (e.g., only East or only West). Across specific timescales (session based alignments, comparisons of trial types, within trial epochs), dHPC associates differentially with all three temporal categories. Across a session, we observe a decrease in theta and beta power before, and an increase in theta power after, the target strategy changes. Beta power is increased around the point at which rats learn the current rule. Comparing trial types, on trials before a rat has learned the correct strategy, beta power is increased. Within a single trial, after an incorrect (but not correct) choice, beta and gamma power increase while the rat returns to start a new trial. If gamma (but not beta) power was high during this return, the rat is more likely to make a correct choice on the next trial. On the other hand, low gamma power during the return is associated with incorrect trials. dHPC, therefore, appears to track task demands, with the strength of each rhythmic frequency differentially associating with specific behaviors across three distinct timescales.

Women with inflammatory bowel disease (IBD) report changes in symptoms due meses and hormonal contraception. However, research on the impacts of menopause on IBD symptoms and progression in women is limited. We systematically reviewed existing literature to describe the impact of menopause, menopause transition, and hormone replacement therapy (HRT) on IBD activity, symptoms severity, and progression. Our search strategy included terms related to menopause and IBD. PubMed, CINAHL, PsycINFO, Embase, and Web of Science were searched. Two reviewers screened all records. Findings were reported using narrative synthesis. Out of 1568 identified records, we reviewed 107 full text reports and included 14 studies (5 cohort, 3 case-control, 5 cross-sectional). IBD participant sample sizes ranged from 37 to 1367. Five studies examined the relationship between menopause/menopause symptoms and disease activity, with four reporting no relationship and one reporting more bothersome menopause symptoms in women with active IBD, compared to those in remission. Seven studies examined the impact of HRT on IBD risk or symptoms: HRT associated with increased risk of IBD (n=2), no change in IBD symptoms (n=3), and improvement of IBD symptoms (n=2). Five studies examined menopause onset age for IBD patients: earlier menopause onset in IBD participants compared to age-matched controls (n=4), no difference in menopause onset (n=1). Few studies have examined the effects of menopause, menopause transition, or HRT among IBD patients. Inconclusive results were found for the relationship between menopause and HRT and IBD progression, symptoms, and risk. Some evidence suggests that women with IBD may have an earlier onset of menopause compared to controls. However, there is a need for continued research on the relationship between IBD disease activity and menopause symptoms to create tailored interventions to improve women’s health in IBD across the lifespan.

Tumor cell survival and recurrence remain a leading cause of death among cancer patients, and it is likely that the residual tumor cells that form the secondary tumor have distinct phenotypes from the primary tumor. The transcription factor NRF2 is thought to play a role in tumorigenesis, metabolic reprogramming, and recurrence in breast cancer. Emerging evidence suggests that NRF2 also intersects with the circadian rhythm, the 24-hour oscillatory clock present in all cells. My project investigates how NRF2 interacts with circadian rhythm genes, and how this interaction affects cancer cell growth. Mouse cell lines NMuMG, EMT6, 66Cl4, and 4T1 were cultured, treated with dexamethasone for synchronization of cellular clock, and harvested over three days. Cell pellets were collected every eight hours after synchronization, for a total of seven timepoints across 48 hours. I performed RNA extraction, cDNA synthesis, and RT-qPCR to analyze gene expression of  NRF2 (Nfe2l2), NRF2 target genes (Nqo1, Slc7a11, G6pdx, Gpx2, Txn1), and circadian rhythm genes (Bmal1, Clock, Per2, Cry1, Per1, Nr1d1) at each timepoint. 66Cl4 cells were further used to perform a CRISPR knockout screen for NRF2 target genes, to investigate which genes are essential for tumor cell viability. I cultured and infected cells with Cas-9 enzyme and sgRNA corresponding to 30 NRF2 targets using lentivirus, then allowed them to proliferate to 14 population doublings over the course of the screen. After the screen had completed, cells were sent for genomic sequencing to identify hit genes. Though these experiments are ongoing, we aim to identify 4-5 hit genes through the screen to direct future research on how NRF2 promotes tumor cell survival and proliferation. My data on NRF2 and circadian clock will also shed light on the intricate role of NRF2 in the cell, and open the door for new therapeutic targets.

Acute Pancreatitis (AP) is a sudden inflammatory condition of the pancreas that can lead to significant mortality. Despite its rising prevalence and associated healthcare burden, treatment options remain limited to supportive care, with mortality rates in severe cases reaching 30%. Activin A is a key contributor to AP, interacting with the ACVR2A receptor to regulate various pathophysiological processes, including inflammation through immune cell recruitment. This study hypothesizes that activin A binds to ACVR2A to activate the ERK pathway, leading to increased NF-κB expression and elevated production of pro-inflammatory cytokines, including TNF-α and IL-1β. Experiments were designed using the 266-6 immortalized pancreatic acinar cell line and RAW 264.7 macrophages. These cells will be cultured for western blot analysis, ELISA assays, and transwell migration assays following activin A stimulation. Lower ERK phosphorylation and reduced NF-κB expression are expected when cells are treated with ACVR2A inhibitors in combination with activin A, compared to activin A treatment alone. ELISA assays are anticipated to confirm increased TNF-α and IL-1β production in 266-6 cells following activin A treatment. Macrophage migratory capacity is expected to increase when exposed to conditioned media from activin A-treated 266-6 cells. These findings will provide insights into the role of activin A in AP pathophysiology, potentially identifying new therapeutic targets for mitigating pancreatic inflammation and immune cell recruitment.

In the video game Stardew Valley, the player leaves their corporate job behind to live as a farmer in the countryside, where they manage their farm, battle monsters, and build relationships with townspeople. Importantly, the aforementioned means players play at labor, spending numerous in-game hours doing physical labor (e.g. chopping down trees, tending their farm, fighting monsters) and emotional labor (e.g. giving townspeople gifts, dating). Therefore, through this project, I explore how the identities and experiences of femme-presenting and feminized people of color (POC) impact their gameplay decisions in Stardew Valley, specifically how and why they play at physical and emotional labor. The term "femme-presenting" can apply to anyone who is perceived as feminine by themselves or by others. The term "feminized" is for people who may not want to come off as femme-presenting, but often still do according to systems/society. Over the course of five biweekly meetings over roughly ten weeks, eight participants play Stardew Valley while I observe and ask questions. By reviewing the recorded gameplay footage and our conversations, I examine what each individual player prioritizes (e.g. aesthetics, narrative, money) and why they do so. My analysis of how participants play at labor relies on an understanding of how being a femme-presenting/feminized POC interacts with their additional various other identities (e.g. sexuality, ability, class) to subsequently influence their gameplay decisions. Anticipated results include participants playing at labor in Stardew Valley for the sake of escapism, a sense of control, and to build community. This study reveals the need for further interventions in video game studies which center cozy gaming spaces, femme/feminized communities of color, and feminist theorizing.

The research project involves designing and building circuits for a pulsed laser and photodetector for a speed of light time of flight measurement device and developing pedagogy and curricula for 200-level experimental laboratory and 400-level senior research project physics courses. We completed project-based learning on circuit principles, Kirchhoff’s Laws, RLC circuits, Thevenin and Norton equivalence, AC signal, phasors, RC filters, oscillators, impedance, diodes, transformers, operational amplifiers, metal–oxide–semiconductor field-effect transistors (MOSFET), and introductory optics and optoelectronics. We performed hands-on training on analog circuits logic and components, CAD design, prototyping, and practical physics applications of analog circuits. Technical lab responsibilities include learning to design analog circuits using a CAD program; ordering the printed circuit board (PCB); testing circuits for functionality, accuracy, and precision; testing the speed of light measurement device for precision with light passing through air and other mediums; and measuring the refractive index of different mediums. Physics education responsibilities include incorporating our work into BPHYS 231 Experimental Physics Speed of Light Lab; developing a pre-lab quiz and lab manual; and providing documented guidance for students on learning objectives, instructions on use of the new speed of light device, lab extensions for BPHYS 231 final projects, and research topics for BPHYS 433 Senior Project. Due to the large scope of this project, the research will continue through Autumn 2025.

Tuberculosis (TB) remains a major global health challenge, causing over a million deaths annually despite being a curable disease. A critical issue is treatment non-adherence, as many patients struggle to complete the required six-month regimen due to a lack of support and access to reliable medical guidance. Improving treatment adherence can significantly increase recovery rates and save lives. This project develops an AI-augmented chatbot powered by GPT-based models to assist Spanish-speaking TB patients. This is done by providing accurate medical guidance, fostering empathy, and enhancing communication between patients and healthcare providers. Integrated into a Human-System Interaction (HSI) interface, the system employs three AI models: a two-step pipeline that classifies messages as informational or emotional to tailor responses appropriately, a few-shot model that generates responses based on examples from prior patient interactions, and a Retrieval-Augmented Generation (RAG) + few-shot model that retrieves relevant medical information from guidelines while maintaining conversational fluency. These models leverage the same underlying technology as ChatGPT, optimizing responses for accuracy, linguistic fluency, and empathy. As part of the research team, I contributed to model development and implementation, ensuring alignment with medical guidelines and human-centered design principles. The chatbot is currently undergoing external evaluation by a multidisciplinary team, including healthcare professionals specializing in TB treatment and AI researchers. Evaluators interact with the chatbot using personas as TB patients, asking medical and support-related questions to assess response quality. They rate the system based on medical accuracy, linguistic fluency, empathy, and other key criteria relevant to patient-provider communication. Insights from this evaluation will guide future refinements, with the goal of improving AI-driven patient support systems in clinical settings.

Alzheimer’s disease (AD) is a progressive neurodegenerative disease that affects millions of people. Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive stimulation typically used in psychiatric conditions such as depression and anxiety. rTMS works by using an electric current to generate a transient magnetic field, depolarizing neurons in a target region and creating lasting changes in brain connectivity via synaptic plasticity. Patients with AD show disruptions in the Default Mode Network (DMN), a network of brain regions typically active during rest and crucial for memory consolidation. We hypothesize that strengthening the DMN through rTMS targeted at the left Brodmann 8AV region, selected for being an easily accessible node of the DMN, will improve memory in AD patients. To test this hypothesis, we are conducting a single-blind, single-arm, randomized cross-over trial of rTMS on early-stage AD patients over a 12 week period with week 1 where we scan for the 8AV region via MRI, during week 3 and 8 being the placebo or treatment week. We measure our primary outcome of the participants’ speed of forgetting —a novel index of memory function—through an individualized, adaptive memory test. To eliminate potential confounding variables, we also measure depression and anxiety symptoms during the 1st, 8th and 12th week of the study. Additionally, functional MRI scans will be analyzed for potential structural or functional differences caused by treatment. Preliminary results from our initial participants have shown promising improvements, and we are hopeful that similar outcomes will be observed in the remaining participants. Successful results would provide a novel target for AD treatment using rTMS, and support further investigation of rTMS as a viable treatment option.

The quantum magnetic particle imaging platform (MagPI) is a quantum sensing method that utilizes an ensemble of nitrogen vacancy defects in diamond as a sensor to measure magnetic fields and perform magnetometry. The MagPI experiment currently aims to measure the bend stiffness of DNA through detecting the magnetic fields of an externally applied field and the magnetic moment of a magnetic nanoparticle that has been tethered to our diamond sensor with DNA. This method requires characterized ferromagnetic particles with a size on the order of 10 nanometers and magnetic moments on the order of 10^-18 Am², the latter of which is information that suppliers and producers do not categorize or are able to obtain for singular particles. We will use MagPI and optically detected magnetic resonance to perform vector magnetometry and image the magnetic dipole moments of different magnetic nanoparticles and calculate their magnetic moments. In particular, we will compare TurboBeads, which were the 30 nanometer carbon coated metal particles previously used for this experiment but are no longer obtainable, and 30 nanometer Co-Zn ferrite beads from a collaborator from Sandia. We aim to detect, accurately measure, and categorize the properties of singular magnetic nanoparticles to identify promising particles to use for our experiments. We will compare these two nanoparticles and their properties for MagPI applications. The results of this project will be used for experiments using the MagPI platform, and showcases a method to measure the magnetic moments of singular particles for future use in research projects.

The kappa opioid receptor (KOR) system is a promising target for substance use disorder, yet its role in long-term addiction regulation remains unclear. This project investigates how selective activation of the KOR/c-Jun N-terminal kinase (JNK) pathway activates the enzyme peroxiredoxin VI (PRDX6), triggering the release of reactive oxygen species (ROS) and resulting in long-lasting KOR inactivation distinct from its canonical Gαi pathway. I investigate whether JWT-101, a repurposed ligand, acts as a long-term KOR antagonist by inducing JNK-mediated ROS production, potentially offering new therapeutic avenues. KOR-Cre mice were injected in the prefrontal cortex with oROS-Gr, a fluorescent tag that senses ROS concentrations, for selective expression in KOR-positive neurons. Using high-resolution two-photon microscopy, I monitored ROS levels in live brain slices after 2 weeks from these mice. Bath application of JWT-101 led to increased fluorescence, indicating elevated ROS production and thus, JNK activation. To confirm JNK path specificity, I applied MJ33, an inhibitor of PRDX6. Fluorescence was reduced following MJ33 treatment, indicating that JWT-101 acts in a KOR/JNK manner. These findings suggest that JWT-101 induces KOR inactivation through ROS-mediated signaling. This research provides insights into KOR/JNK signaling in substance use disorders, with implications for developing targeted therapies for recovery and relapse prevention.

The health risks of particulate matter measuring less than 2.5 micrometers (PM2.5)  include: respiratory disease, cardiovascular issues, and cognitive impairments. Its presence near schools and colleges remains underexplored. This study examines the relationship between PM2.5 exposure levels and academic outcomes in community colleges located in historically redlined neighborhoods across four major West Coast cities: Los Angeles and San Diego in California; Portland, Oregon; and the greater Seattle area in Washington. Using data from the PurpleAir Network, state air quality indices, and community college governing bodies, we analyzed and compared PM2.5 levels near institutions located within historically redlined neighborhoods and institutions located outside those neighborhoods. Leveraging the Python programming language and Google Colab, we examined correlations between an institution’s demographic makeup and transfer rates relative to PM2.5 exposure. Data sets obtained were filtered between the hours of 8 AM and 1 PM during the months of January 2024 through December 2024. Our findings indicate a correlation between higher PM2.5 exposure and lower academic performance for colleges serving predominantly racially marginalized communities located within historically redlined neighborhoods. This research reinforces the role of environmental inequities in shaping educational disparities and highlights the need for targeted policies to address air quality in affected communities.

The external fertilization and transparent embryos of zebrafish make them an informative model of vertebrate embryonic development from the 1-cell stage. In this study, we examine the impact of de novo GTP synthesis on the formation of the embryonic somites, which are embryonic cells which develop into segmented blocks of muscle that run the length of the body. We hypothesize the de novo GTP synthesis is required for the correct patterning of somite borders in zebrafish embryos, and that this process facilitates the formation of a vertebrate body plan. Inosine monophosphate dehydrogenase 2 (IMPDH2) is the enzyme which catalyzes the conversion of inosine monophosphate (IMP) towards the de novo synthesis of GTP instead of ATP. To test the impact of de novo GTP synthesis on somite formation, we inhibited IMPDH2 function with mycophenolic acid (MPA) both before and after somite formation began. MPA caused stronger defects in the somite morphology and embryonic body shape when added to embryos before somite formation began, earlier in development. We performed in situ hybridization against xirp2a to assess the effect of inhibiting IMPDH2 function on the formation and patterning of the somite borders. MPA treatment decreased the definition of somite borders we could observe in the posterior tail. Inhibiting IMPDH2 with MPA produced somites with smooth, round borders instead of the chevron-shape typical of zebrafish. We next conducted immunohistochemistry against IMPDH2 to examine the expression and localization of this enzyme in embryonic cells when GTP conditions are low. In MPA-treated embryos, we observed increased expression of IMPDH2 across the entire embryo. We will next explore how GTP abundance affects activity of the clock, a mechanism which synchronizes gene expression of embryonic cells.

The identification of synergistic drug combinations remains a significant challenge in oncology due to the large amount of existing drugs and complex interactions between these drugs. In this work, we propose an active learning framework applied to the NCI ALMANAC dataset to efficiently uncover promising drug pairs that conventional screening methods might overlook due to lack of time and resources to handle these nearly countless combinations. Building on established greedy sampling strategies—such as GSx, which selects samples based on maximal minimum distance in the input space, and GSy, which focuses on output diversity—we introduce modifications to potentially enhance sample selection diversity and predictive performance. First, we explore replacing the traditional greatest minimum distance criterion with a greatest average distance metric, hypothesizing that this adjustment captures the overall variability in the data differently than the traditional method. Second, we redefine the improved greedy sampling (iGS) approach by standardizing the distance metrics from both the input (GSx) and output (GSy) spaces using Z-score normalization (or alternative standardization methods) prior to their aggregation, rather than combining them multiplicatively. We conduct a comprehensive comparative analysis against traditional methods to evaluate improvements in model convergence, prediction accuracy, and the ability to identify rare but potent drug combinations. We also explore other active learning strategies as Query By Committee (QBC) and others. Our preliminary findings suggest that these tailored active learning techniques offer a promising pathway toward more efficient and insightful exploration of high-dimensional drug interaction landscapes.

Before a child says their first word, they begin to produce and practice sounds they hear. Early vocalizations play a crucial role in speech development and language acquisition. However, most research on infant vocalizations focuses on children in Western, industrialized societies. This study contributes to the growing body of literature on diverse linguistic environments, specifically examining emergent sounds in the Panãra community, an Indigenous group in the Brazilian Amazon with approximately 700 speakers. Ten infants aged 2-21 months wore recording devices that collected a recording of their language environment over a day. Alongside shared ethnographic observations, I manually annotated selected 30-second audio segments for a fine-grained analysis of child vocalizations. I am currently analyzing the frequency and types of child vocalizations (i.e. vocal play, canonical babbling, variegated babbling) in infants' speech, and I plan to explore how these vocalizations may differ across the age range studied. I predict that child vocalizations will become more complex with increasing age, following pre-speech vocal development stages broadly found across cultures. My findings will contribute to a broader understanding of how language learning varies across cultural settings, vocalization stages, and the role of the environment to language development. 

This research study explores the evolutionary adaptations of the TLR7 protein receptor in primates in relation to Flavivirus (Yellow Fever) recognition. TLR7, an important receptor in the immune system, is essential for recognizing single stranded RNA viruses such as Flavivirus. Given the growing prevalence of Yellow Fever in tropical climates, I hope to understand how environmental factors shape immune response. I hypothesize that ecological niches, particularly wet vs dry climates, play a crucial role in the evolution of the TLR7 receptor among primate species. Since Yellow Fever is transmitted by mosquitoes, which thrive in wet climates, these environments are likely driving the transmission of the virus. As a result, wet climates may exert selective pressure on the evolution of TLR7 to enhance immune responses against Yellow Fever in regions where mosquitoes are prevalent. To conduct comparisons of the TLR7 receptors, I will be running Blast, a bioinformatics software that compares genomic sequences across different species. This tool will allow for identification of both conserved and divergent regions in the TLR7 sequences from primate species, including humans, that inhabit wet and dry climates. These variations could reveal evolutionary adaptations influenced by ecological pressures. Through these sequence comparisons, I aim to explore how differences in TLR7 might affect susceptibility to Yellow Fever and other similar viral infections. Understanding how ecological conditions shape immune receptor evolution could also improve our ability to predict how different populations might respond to emerging infectious diseases.

Dynamic marine environments require long-term spatiotemporal datasets to successfully monitor and understand patterns in ecosystem composition on a decadal scale. High-resolution photography is often used to compensate for the field logistical constraints associated with marine sites, such as personnel availability or weather conditions, and works well to quickly capture data in the field. However, these photos require extensive manual analysis after the fact. As a research mentee, I asked the question: “Can image annotation with machine learning models provide enough clear data to inform community ecology studies of sessile organisms in subtidal habitats?” Using images collected through transect/quadrat sampling by the Sebens Lab’s Salish Sea Long-term Monitoring Project (University of Washington Biology and Friday Harbor Laboratories), a variation of an open-source model (CoralNet) was trained in the identification of relevant sessile flora and fauna. I then used CoralNet to continue the work of the lab by generating sessile assemblage metrics for a single site in the Friday Harbor Laboratories Biological Preserve. This site included images from transects at two different depths, with sampling from 2014 and 2024. After being uploaded, CoralNet identified 200 random points per image to the lowest possible taxon. I then reviewed all annotations for accuracy and corrected them whenever necessary. This technique greatly reduced the time spent per identification, without sacrificing accuracy. Next, I calculated species richness and Simpson’s Diversity for each quadrat and transect, comparing between depth and year. My analysis showed significant increases in both metrics from 2014 to 2024 and no significant differences between depths, demonstrating a successful report on the dynamics of a subtidal marine community. Application of this method to the entire existing dataset (7 sites, 63 transects per year), and others, provides opportunities to streamline analysis of sessile community composition.

Surf smelt (Hypomesus pretiosus) are ecologically and culturally important forage fishes that rely on intertidal beach habitat for spawning. However, the combined effects of rising sea level and human modification (e.g. seawalls, bulkheads, riprap) have put this habitat at risk of coastal squeezing, which could reduce available spawning areas along Puget Sound. This research aims to assess the vulnerability of surf smelt spawning beaches to climate change by combining field data collection with quantitative analysis. We evaluated existing risk assessment methods, such as the Coastal Vulnerability Index (CVI) to determine its applicability to Puget Sound. Additionally, we conducted beach surveys at productive spawning beaches to characterize the beach morphology. Our morphodynamic analysis included measurements of beach slope, sediment composition, pH, and water table depth from the high tide line to the waterline. Our hypothesis suggests that spawning beaches with a lower slope, smaller sediments, and a shallow water table will be more resilient to climate change impacts. Findings from this study will improve our understanding of climate-driven and anthropogenic threats to intertidal ecosystems and provide insight into habitat resilience, supporting conservation efforts for surf smelt populations.

Dementia, a growing global health concern, affects the nervous system and leads to severe cognitive impairment, with Alzheimer’s disease (AD) being the most common form, currently impacting nearly 7 million Americans. As life expectancy increases, the prevalence of dementia increases in corresponding fashion, driving research efforts like those of the Darvas Lab, where we study AD and other related dementias using adeno-associated viruses (AAVs) to induce neuropathologic changes. The TDP43 protein is involved in neuropathologic changes such as those in Frontotemporal Dementia (FTD) and in Amyotrophic Lateral Sclerosis (ALS), a primary motor neuron disorder. TDP43, primarily localized in the nucleus, plays a crucial role in regulating gene expression and RNA metabolism. TDP43 pathology in neurons involves the presence of TDP43 in the cytoplasm and its accumulation in cytoplasmic inclusions. To better understand the role of TDP43 in neurodegeneration, we use a mouse model where TDP43 proteins are introduced via AAV, a genetically engineered viral vector commonly used in research. This approach allows control over the timing of neuropathologic changes. Our prior AAV constructs included the Synapsin I promoter, which led to a severe ALS-like motor phenotype due to its expression in spinal motor neurons. However, this model could not be used to study the more subtle effects of dementia due to the extreme nature of the physical pathology. Therefore, our goal is to produce a new model to overexpress TDP43 using an AAV that is exclusive to the cortical brain regions relevant to FTD by instead including the CamKIIα promoter, which exclusively drives expression in the forebrain. I assessed behavioral phenotypes in our mouse model by conducting a Y-maze to evaluate effects on short-term memory, and analyzing neurological scoring to evaluate neuromuscular dysfunction. The development of a more dementia-focused TDP43 model will allow us to more specifically investigate its neuropathology.

Relative Risk (RR) is a highly interpretable parameter in epidemiology and biostatistics, based on both binary input and outcome. It is frequently used in vaccine development to measure the relative efficacy between two treatment groups.
Researchers are often tempted to use generalized linear models (GLMs) to estimate the logarithmic RR with respect to a set of baseline covariates. However, this approach has inherent flaws, as GLMs do not account for variation dependence in Relative Risk on its nuisance parameters. Richardson et al. have developed an unconstrained and variation-independent doubly robust nuisance model using the log Odds Product (OP).
To expand on this work, we will explore alternative nuisance models—both those developed by us and those from other researchers—and compare their computational robustness to that of the log Odds Product (OP).
Additionally, using the brm R package (which streamlines the methods proposed by Richardson et al.), we will analyze a dataset where Relative Risk serves as the target of inference and compare these results to those obtained using regression methods.

Global interest in and demand for macroalgae farms has increased due to growing interest in seaweeds as food, biofuel, a possible source for carbon sequestration, and an economic asset for small island communities. However, the presence of farms can negatively impact marine mammals, with risks including entanglement, habitat exclusion, and behavioral changes. In this study, we conducted passive acoustic monitoring over three years (2021-2024) in developing macroalgae 5-line and catenary farms at Romero and Media Luna reefs off the southwest coast near La Parguera, Puerto Rico, to assess the long-term effect on bottlenose dolphin (Tursiops truncatus) movement and behavior in the region. Detections were automated using PAMguard software and manually confirmed with visual validation by trained acousticians. We observe higher interaction with farms at dawn and dusk, which corresponds with the crepuscular nature of T. truncatus. To date, we observe no entanglements, and our models indicate no significant long-term effect on the local bottlenose dolphins at low macroalgae biomass. As biomass increases, this may change. This research highlights the important trade-offs between economic development and conservation and the promise of passive acoustic monitoring as an effective, data-rich tool for managers. 

Sound is a vibration that is created by an oscillating object and travels in periodic waves of pressure through a medium. Sound waves are characterized by properties such as frequency, amplitude, wavelength, and speed. The purpose of my research was to measure the effects the lower temperature and air pressure present in the stratosphere have on the properties of sound. To conduct this research I custom-designed an Arduino based sensor with a barometer and thermometer that was then attached to a weather balloon. The sensor also had a buzzer that repeated a tone at constant intervals along with a microphone that measured the amplitude of sound across various frequencies as it was necessary to consider the impact that the high wind speeds present in the stratosphere would have on the measurements. As the air becomes colder and less dense it also becomes less elastic causing it to transfer energy less efficiently which in turn leads to a decrease in amplitude. Frequency, however, did not change as it is determined by the source of the sound and does not depend on the properties of the medium. Understanding how changes in the properties of the medium affect the properties of sound opens a path to using sound to illuminate the properties of the medium. Additionally, broadening our understanding of how various atmospheric conditions present on our own planet affect the properties of sound deepens our understanding of how the various atmospheric conditions present on other planets will impact the properties of sound.

Mycobacterium abscessus is a non-tuberculous mycobacterial (NTM) species that causes severe pulmonary infections, particularly in immunocompromised patients and those with preexisting lung diseases such as cystic fibrosis. Treating M. abscessus infections is challenging due to its intrinsic antibiotic tolerance and capacity to develop multidrug resistance. To identify novel molecules that can target this pathogen and enhance current treatments, we screened a library of FDA-approved drugs (n = 2,400). Our data shows that Netupitant, a drug commonly used to prevent chemotherapy-induced nausea and vomiting, exhibits potent antibacterial activity against a broad range of M. abscessus clinical isolates, including multidrug-resistant strains, with a minimum inhibitory concentration (MIC) ranging from 4 to 16 µg/mL. Furthermore, in combination with amikacin, a standard treatment for M. abscessus infections, Netupitant demonstrated strong synergistic interactions, as confirmed by checkerboard microdilution and time-kill assays. These findings highlight Netupitant’s potential as a novel therapeutic option for M. abscessus, particularly in combination with existing antibiotics. Future studies exploring its mechanism of action and in vivo efficacy could further advance antibacterial drug discovery for difficult-to-treat NTM infections.

Menopause is a significant life transition that is experienced differently across cultures, with each cultural background shaping unique beliefs, expectations, and responses to menopausal symptoms. Among Somali and Indonesian older adults with a uterus, cultural factors play a particularly influential role in shaping the menopause experience, potentially affecting symptom recognition, coping strategies, and interaction with healthcare providers. The purpose of this qualitative study is to 1) explore menopausal symptoms, perceptions, beliefs, and experiences of aging and menopause among Somali and Indonesian older adults, and 2) examine how cultural factors shape their understanding of menopause, as well as how they interpret and manage the symptoms associated with this stage of life. We conducted a cross-sectional qualitative study using semi-structured interviews with 5 participants with a uterus: 2 Somali and 3 Indonesian individuals. We recruited participants through community networks within Somali and Indonesian populations living in Washington state. We included individuals who are 1) 60 years or older and 2) undergoing or have gone through menopause. We chose older adults for their reflective perspective, offering holistic insight into the long-term impact of menopause and their ability to share cultural wisdom and experiences. Our findings will inform healthcare providers in delivering culturally sensitive care to support individuals going through menopause in these communities. Additionally, this knowledge can inform the development of targeted interventions and educational tools that help bridge cultural gaps in menopause understanding, thereby promoting holistic, culturally sensitive, and inclusive care for older adults with menopausal symptoms in these communities. Addressing these deficits can lead to improved care for Somali and Indonesian adults with a uterus while also benefiting women more broadly by promoting a more comprehensive and inclusive approach to menopause support.

Glaciers have long been used as the bellwethers of climate change, given their ability to store gases, dust, microbes, and other environmental materials in their layers; tracking their recession has also been an important visual indicator of climate change. In this research, I examine how anions in newly exposed vary with depth. To do this, I took samples from exposed vertical ice faces on the Coleman glacier, on the north face of Mount Baker. Samples were thawed and analyzed using ion chromatography.  Trace amounts of chloride, nitrate, sulfate, and phosphate were found in each sample. The ion concentrations showed no trend with depth, and the ice itself appeared uniform. This is in contrast from vertical cores taken from solid ice in numerous other surveys, which show distinct annual layers and variation. This suggests that the ice at vertical faces has different properties from that at the top layers, including in its ability to trap environmental markers. Further research is needed to confirm this difference and examine which of these markers is most affected. Increased understanding of these markers could give more insight into how glaciers change over time and interact with their environment.

The Sensors, Energy, and Automation Lab (SEAL) aims to gamify undergraduate research by instituting a leaderboard, awarding points for tasks, assigning ranks for accomplishments and published papers, and framing research directions as Quests. Individuals receive a character sheet with a health bar, while groups compete against one another in Racetrack- a software for team challenges. Gamification in educational settings is well-studied: gamifying learning can boost students’ motivation, retention, and challenge appraisal. However, research indicates that the efficacy of gamification varies dramatically, particularly personality traits like extraversion, which correlate more positively with success in software with leaderboards. Significant gaps exist in gamification literature; existing research primarily studies gamification in classrooms, not workplaces or research environments. Further, the studies fail to incorporate modern approaches to psychology. The socio-psychological model suggests personalities and behaviors differ depending on the environment, meaning people may exhibit different personality traits in gamified environments. Moreover, gamer motivation, a personality test tailored to predicting player personality with strong correlations to the Big Five (psychological scale for key personality traits), has yet to be tested in gamification studies. By accounting for contemporary psychological theory, SEAL aims to rigorously test the hypothesis that gamification is an effective structure in lab organizations through multi-year longitudinal study on a scale never seen in gamification literature. SEAL’s large cohort and gamified structure offer a perfect platform to analyze the role of demographic and personality type in gamification outcomes. Our preliminary results explored collected qualitative and quantitative data on demographics, gamer motivation personality, and perceptions of the SEAL system by anonymously surveying 81 associates. Our longitudinal study contributes to the growing literature on gamification; a solution potentially improving productivity in research ecosystems.

In the paper "Planting Undetectable Backdoors in Machine Learning Models" by Goldwasser et al (arXiv:2204:06974), the authors establish the notion of "black-box undetectability" for machine learning models and prove it in many cases. This is a backdoor that is undetectable by merely looking at inputs and outputs of the model. The paper also introduces the concept of "white-box undetectability."  We aim to consider this stronger notion and outline how even with the knowledge of entire model weights, there may be undetectable backdoors in a model. More specifically, we establish an idea where one takes an innocuous model (say a Multi-Layer-Perceptron model) and enlarges it by adding "dummy" edges and using appropriate non-linear activation functions to effectively place a backdoor in the model. In our project, we establish a proof of concept by backdooring an MNIST classifier.

Latine people constitute the largest minority in the US, yet the prevalence of diabetes within the Latine community is nearly twice that of White Americans. Latine populations also experience food insecurity at higher rates than the national average, which heightens their risk for chronic conditions like type 2 diabetes (T2D). While nutritional counseling is critical for T2D care, there is limited research on the barriers to effective counseling, especially for minoritized identities. Understanding how Latine patients relate to counseling and barriers to adherence is an urgent health concern with significant implications for addressing health disparities. This study investigates both micro (e.g., provider pathologization of culturally relevant foods) and macro (e.g., food access) barriers to following nutritional guidance for Latine people with T2D. Previous research in South Asian communities shows providers pathologize culturally relevant foods, leading to poor metabolic control, increased complications, higher healthcare costs, and lower quality of life. Food insecurity exacerbates outcomes, with food-insecure diabetic patients reporting less control over their diets despite understanding dietary requirements. However, these barriers remain unexplored for Latine people with diabetes in the US healthcare context. Through a qualitative study in Greater Seattle, we seek to understand the experiences of Latine people managing T2D by conducting structured interviews on barriers to following nutritional counseling. Content analysis uncovers themes related to micro and macro barriers. We aim to enhance culturally competent healthcare to overcome barriers preventing Latine people with T2D from following nutritional guidance. By amplifying the voices of Latine patients, we can inform providers on more effective ways to interact with this population and develop tailored care plans.

Due to considerations such as dose reduction, or physical limitations of the scanner, computed tomography (CT) images must sometimes be reconstructed from sparse-view or limited-angle sinogram data, resulting in a loss of image quality. In recent years, there has been a great deal of interest in using neural networks to improve image quality in these scenarios. In this work, we implement three neural network architectures – denoising convolutional neural network (DnCNN), U-net, and transformer – and apply them to sparse-view and limited angle problems in both a post-processing and iterative, “plug-and-play” reconstruction context. In post-processing, the neural network is applied to the final image to remove artifacts, while in the plug-and-play approach, it is incorporated into the algorithm that reconstructs the image from the sparse-view or limited-angle data. Based on standard image quality metrics, the post-processing approach with the U-net is found to give the best image quality. The plug-and-play approach, while not always providing the best image quality, is able to ensure fidelity with the sinogram data.

The widespread use of makeup raises concerns about bacterial contamination, which can lead to acne, rashes, pink eye, and staph infections. Despite these risks, hygiene practices in cosmetic use, especially in public settings, are often overlooked. This study investigates bacterial contamination in both personal makeup products and in-store testers to assess potential health risks. Swab samples were collected from used personal cosmetics and store testers at popular beauty retailers, focusing on mascaras, foundation bottles, lipsticks, and sponges. Samples were transferred to nutrient-rich media plates, incubated at 37°C for 24–48 hours, and analyzed through colony-forming unit (CFU) counts and Gram staining for bacterial classification. Preliminary results suggest that store testers contain higher bacterial loads than personal products, emphasizing the need for improved hygiene practices in retail environments. These findings could encourage cosmetic brands and retailers to implement better sanitation protocols, such as stricter single-use applicator policies or improved packaging designs, to limit bacterial contamination and promote safer cosmetic use.

My research project focuses on age-related changes in muscle function. We have previously designed and used novel young and naturally aged in vitro three-dimensional engineered muscle tissues (3D-EMTs) using donated myoblasts from the Study of Muscle, Mobility, and Aging (SOMMA) to investigate this. A question raised in this research is the how closely force measured in 3D-EMTs correlates to in vivo force of intact skeletal muscle. To address this, I stimulated young and aged mice's gastrocnemius muscles to contract (Aurora Instruments) measuring maximum force, contraction/relaxation kinetics, and fatiguability. Mice were then sacrificed and hindlimb muscles dissociated to isolate skeletal muscle myoblasts for cell culture. Myoblasts were amplified and used to generate young and aged rodent 3D-EMT. We tested in vitro 3D-EMT muscle mechanics using a Magnetometric Analyzer for engiNeered Tissue ARRAY (MantARRAY, Curi Bio). In vitro muscle force data was compared to in vivo force data from the same mouse. Results generated by this project helped identify the correlation between in vivo and in vitro force measurements and how they are impacted by age. This study also allowed us to bank multiple cell lines for future high throughput studies to utilize these rodent 3D-EMT models to study the progressive loss of muscle mass and function known as sarcopenia. The results from this project and the cellular models created will be used in the future to investigate potential targets for therapeutic interventions to treat sarcopenia in an ever-expanding aging population.

Hemophilia A (HemA)—a severe genetic bleeding disorder affecting 1 in 10,000 people—is caused by mutations in the F8 gene. These mutations cause an inability to produce the coagulation factor eight protein (FVIII) necessary to stop bleeding after a wound. Current treatment- repeated FVIII replacement, is costly and frequently ineffective, as around 30% of patients develop inhibitor antibodies causing the immune system to reject the foreign protein. Alternatively, our lab hopes to utilize gene therapy to restore the functional gene and allow the body to continue producing the essential FVIII protein itself. 45% of human HemA cases are caused by a mutation of the human F8 gene where a large portion called Intron 22 (In22) is inverted. The In22 inversion halts translation of the rest of the gene, and the resulting FVIII protein is truncated and non-functional. To address the mutation, our lab aims to use a CRISPR-based knock-in approach to the DNA following In22, upstream of the mutation site. We expect that this strategy can restore endogenous production of missing FVIII and potentially provide curative treatment for affected patients. To test this treatment’s efficacy, this project utilizes a HemA mouse model (E16) in which a neo cassette insertion at the 3’ end of exon 16 disrupts FVIII expression. We propose using the same strategy to integrate the missing DNA upstream of the mutation and restore FVIII function in HemA mice. I use molecular cloning to construct and evaluate different versions of the CRISPR-Cas9 plasmid containing sgRNA, and a plasmid containing the donor DNA. This research allows us to determine the safety and efficacy of our gene therapy strategy, and evaluate how to maximize recovery of FVIII production. This project aims to eventually contribute to treatment of human HemA patients, without the expensive and unreliable replacement of the protein.

My project aims to improve sanitation in mental health and maternity hospitals in Ethiopia by introducing pressure-washing cleaning services. This initiative goes beyond routine cleaning, it restores dignity and safety to healthcare facilities where poor hygiene discourages patients particularly expectant mothers from seeking essential care. By reducing contaminants and improving cleanliness, the project will create a more welcoming environment that encourages hospital births rather than home deliveries driven by unsanitary conditions and odors. To achieve this, I am providing pressure-washing equipment to underserved hospitals and clinics focusing on four hospitals and three clinical facilities in urgent need of sanitation improvements. Additionally, I am engaging with smaller underserved clinics that play a vital role in delivering essential healthcare services to their communities. This project presents multiple challenges including identifying high-need facilities managing equipment distribution and coordinating regular cleaning schedules. I am actively involved in every aspect from logistical planning to hands-on implementation. My role requires strong project management and problem-solving skills to ensure a tangible impact with limited resources. Beyond logistics, this work demands an understanding of the experiences of vulnerable patients. Effective communication with hospital staff and government officials is crucial for building trust and aligning our efforts with their priorities. This experience is helping me grow as a leader improving my ability to mobilize communities around a shared goal while remaining sensitive to cultural and systemic challenges. Ultimately, this project is about more than sanitation—it is about transforming healthcare spaces into environments where patients feel safe respected and encouraged to seek the care they need.

As Cannabis use is becoming more widespread there is growing concern regarding the respiratory exposures of employees working in indoor cannabis processing facilities. Employees in these occupational settings are frequently exposed to volatile organic compounds (VOCs), particulate matter (PM), other respiratory irritants, and allergic sensitizers. These exposures are linked to work related illness and disease, such as occupational asthma. Notably, a fatality, in 2022, in a Cannabis worker due to occupational asthma highlights the urgent need for improved exposure controls. Cannabis processing workers experience prolonged and frequent exposure via inhalation with little knowledge on the respiratory hazards of this work. This study aims to evaluate the efficacy of a local exhaust ventilation (LEV) system to reduce exposure to airborne hazards during automated joint filling. Automated joint filling is a common process in Cannabis production facilities, using mechanized equipment pre-ground material is dispensed into pre-rolled cones. This method is preferred in the field as it increases both consistency and efficiency. Over a ~2-hour sampling period across eight batches of pre-rolled joints, we conducted gravimetric sampling for inhalable PM using two inhalable aerosol samplers (IOMs) positioned at the workbench and in the breathing zone. VOC exposure was assessed using thermal desorption tubes and photoionization detectors (PIDs), while continuous respirable PM concentrations were measured using a Nanozen DustCount monitor. Testing air concentration for PM and VOCs with and without the LEV mechanism is being conducted to determine its effectiveness at reducing exposure. We hypothesize that this may be an effective solution, as the LEV has controlled these agents significantly in other similar workplace settings. As this field grows due to recent state by state legalization of Cannabis, these findings hold great impact for workplace safety regulation and solutions. Additional research should be gathered on long-term exposure effects and preventive mechanisms.

The increasing concern over global warming has driven interest in clean energy solutions, with piezoelectricity emerging as a promising alternative. Piezoelectric materials generate electric voltage under external mechanical forces, offering an innovative method for energy harvesting. This work derives a system of partial differential equations (PDEs) and their accompanying boundary conditions that describe the coupled elastic-electric behavior of an Euler-Bernoulli piezoelectric beam. Under the quasi-static approximation for the electrical field, the assumptions of Euler-Bernoulli beam theory, and the constitutive relations for the 3-1 piezoelectric coupling mode (i.e., voltage is generated in a direction perpendicular to external mechanical force), we develop a Hamilton’s variational principle to derive the governing equations and boundary conditions for the piezoelectric Euler-Bernoulli beam. The obtained equations consist of Gauss’s law of electrostatics and the Euler-Bernoulli beam equation that are coupled due to the piezoelectric effect: apparent electric charges that depend on elastic deflection appear in Gauss’s law, while apparent mechanical forces and moments that depend on the electric potential appear in the Euler-Bernoulli beam equation and its boundary conditions. The derivation from first principles, as well as the study of the governing equations constitutes a fundamental framework for analyzing piezoelectric beam behavior, with implications to the improvement of design of piezoelectric energy harvesters.

Multidrug-resistant cancers is responsible for over 90% of the metastatic cancer deaths which show enhanced drug transportation. Our group wanted to know how the acquired drug resistance impacts the flow of the MDR drug class, (Imidazoquinolinone, IMQ) by P-Glycoprotein (transporter protein in helping transport the drug). The experiments were performed by using melanoma cancer cell lines, prostate cells, and mouse genomes as the basis for observation. The cells were then introduced to three derivatives of IMQ, called Imiquimod (IMQ), Resiquimod (RSQ), and Gardiquimod (GDQ). The findings we hope to see were how effective each derivate of IMQ were in transport, hindering cell replication, and rhodamine concentration (compound dye in the cells to see how much of the drug is in the cells) with GDQ expected to have the lowest effect of drug resistance. The future of small molecular immunotherapy prodrugs heavily depends on the research and investigation of candidate compound classes and its derivatives to make sure that it is safe, effective, and the overall quality for the patients.

Dense-core vesicles are membrane-bound structures that carry neuromodulators such as insulin, dopamine, and serotonin. The peptides within dense-core vesicles are initially larger precursor proteins that undergo enzymatic processing to achieve their functional forms. During the defecation motor program in Caenorhabditis elegans, dense-core vesicles released from the intestine harbor neuropeptides that trigger neurons which activate enteric muscles, promoting the act of defecation. Failure of certain proneuropeptides to mature into neuropeptides results in decreased frequency of defecations. CPD-1, a conserved transmembrane carboxypeptidase, is a poorly understood processing enzyme that affects the defecation motor program. I built on our knowledge of EGL-21, another carboxypeptidase known to process neuropeptides and peptide hormones, to better understand CPD-1’s function. I show here that these two carboxypeptidases, EGL-21 and CPD-1, process neuropeptides necessary for successful defecation patterns. Mutants lacking egl-21 had decreased defecation frequency while worms lacking both egl-21 and cpd-1 had an even lower defecation frequency. Additionally, my results show that CPD-1 is expressed in intestinal cells and can compensate for EGL-21’s function. Finally, I am conducting experiments to determine whether one of CPD-1’s targets is NLP-40, an important neuro-like peptide released from the intestine that regulates defecation. These results contribute to our broader knowledge of peptide processing in dense-core vesicles.

This project seeks to investigate the viability of a multi-channel grating coupler (GC) as an approach for individual ion addressing in ion-trap architectures. A multi-channel design is desirable because it allows for one GC to be used for controllable, individual addressing of many ions. Current approaches for ion addressing include bulky optical systems or single channel GCs which both have notable shortcomings. Optical arrays employing large lens and laser systems require complex, error-sensitive setups, challenging the scalability of those systems. Single channel GCs reduce the complexity and footprint of the optical setup, but they are unsuitable for individual addressing of ions within a chain. Single channel GCs provide the ability to globally address N ions using one integrated structure, or individually address N ions using N integrated structures. Both of these solutions are not optimal as global addressing lacks the specificity required for complex quantum operations, and using one grating structure per ion entails a massive footprint for large ion chains, much larger than the chain itself. A multi-channel GC allows many ions to be individually addressed by one compact integrated structure and, with optimization, multi-channel GCs can achieve high coupling efficiencies and low insertion losses, allowing for accurate and reliable addressing of ions. To design a multi-channel GC for this purpose, we first develop an idealized analytical model by deriving the relationship between the incident angle of guided light into a grating structure and the output angle of diffracted light into free space. Using this analytical model, a conceptual design for a multi-channel GC is formulated. Finally, the GC design is optimized using finite difference time domain (FDTD) simulation software. We will present the results of our idealized analytical model and results from optimization of a full FDTD simulation of our structure.

Most human activities engage multiple brain regions simultaneously, but our ability to study this is limited by our capability to run experiments. Electrophysiology is the data-collecting technique of placing electrode probes into the brain to record the electrical activity of neurons. Currently, researchers performing electrophysiology use one or two probes. However, to record activity across many regions, researchers must use multiple probes which introduce new kinds of challenges such as ensuring accurate and reproducible positioning of several probes to target specific areas in the brain, managing probe movements to avoid collisions with each other, and preventing probes from breaking during insertion. Brain-wide coverage will require five, ten, or more probes, amplifying the challenges researchers face with just one or two probes at a time. Over the past two years, I have been developing an automation platform that can solve these challenges in electrophysiology. A key innovation is the integration of a computer-vision-based probe tracking system being developed in collaboration with the Allen Institute. This probe tracking system ensures probes can be accurately positioned on brain regions repeatably and detect when probes fail to insert into the brain, so movements are stopped before damage occurs. The automation platform will also route and manage electrode probes during experiments, preventing collisions with each other and the rig. Together these improvements ensure that electrophysiology experiments can be performed in a reliable, safe, and reproducible manner, but perhaps the biggest improvement the platform provides is efficiency. On average, it takes 15 minutes to insert one probe into the brain, meaning brain-wide experiments using eight probes may need two hours to insert manually, increasing stress on subjects unnecessarily. With automation parallelizing the process, we can reduce insertion times from 15 minutes per probe to 15 minutes flat making brain-wide electrophysiology a viable tool in neuroscience.

Pancreatic Ductal Adenocarcinoma (PDAC) is a deadly disease without prognostic tools for early detection or effective therapeutic strategies. Activin A is a cytokine that is upregulated in tumor and stromal cells that surround the tumor in PDAC and acts as a promoter of metastasis. Activin A has also been shown to stimulate the AKT pathway which is proto-oncogenic. Here, we set out to test the hypothesis that activin A drives PDAC development through the AKT pathway. Western blots for proteins of the AKT pathway (phospho-PRAS40 and phospho-β-catenin) and transwell migration assays will be performed on PanC1 pancreatic cancer cells stimulated with activin A. Additionally, inhibitors of the activin A receptor subtype 2A (ACVR2A) and the AKT pathway will be included to delineate receptor-specific effects. Given activin's known role for simulating the AKT pathway, it is expected that activin A stimulation will phosphorylate and trigger increased migratory capacity of PanC1 pancreatic cancer cells. Inhibitor experiments will confirm that these effects are ACVR2A specific. This data will identify if activin A is a novel therapeutic target in late stage PDAC, a disease with limited targeted pharmacological treatments. 

Manduca sexta is a model lepidopteran insect organism which has been widely used in the field of chemical ecology due to its impressive olfactory senses. Odorant reception plays an important role in locating nectar sources, mating, and ovipositioning. Insects detect volatile chemical compounds (VOCs) present in their complex environment primarily through their sensory organ antenna. Each antenna is made up of thousands of olfactory receptor neurons (ORNs) and each neuron detects specific odor molecules with specific odorant receptor proteins. The whole genome sequencing of Manduca sexta has identified the major chemosensory receptor proteins: odorant (ORs), ionotropic (IRs) and gustatory (GR) but the role of each receptor is still unclear. In this project, we are investigating the role of female-biased odorant receptors OR5 and OR6, which might be involved in detecting VOCs present in their environment and play an important role in mating and oviposition. To investigate the role of these ORs, we have generated mutant strains by using a CRISPR/Cas9 approach and we are checking their effect on odor detection and oviposition behavior by comparing them with wild type strains. We are also performing an RNA-FISH experiment to visualize the ORs and locate the olfactory sensory neurons in the female antennae. In addition to this, we are also working on developing a neurogenetic tool which will allow us to measure the neuronal activity in response to different olfactory stimuli by generating a pan-neuronal BRP-GCaMP6s transgenic line.

Social expectations are constantly changing, and even subjects typically considered “taboo” are changing as well. Though sex is often seen as a private, maybe even secretive, discussion, this lack of public eye to the true nature of sex can lead to many difficulties in an individual's personal and intimate life through misunderstandings and social expectations. This literature review focuses on possible correlations between behavioral sex therapy treatment (such as guided open communication, and sensate focus) and aspects of unsustainable romantic relationships (such as stonewalling and criticism). Some sexual dysfunctions can arise from emotional difficulties, such as anxiety during or before sexual encounters, lack of enjoyment from one or both partners, or different perceived ideas of what is supposed to happen during sex. These difficulties can translate into daily life in the relationship outside of sex. By treating these dysfunctions there may be a domino effect which impacts the relationship outside of sexual relations, which can improve the relationship overall and lead to a relationship that is more sustainable for all parties involved. Through comparisons of articles on treatments typical in behavioral sex therapy and articles defining aspects of unsustainable relationships, like those published by John Gottman, initial findings support connections between the topics. These positive correlations indicate an innate connection between sexuality and relationships, which could lessen the social stigma that surrounds discussing sex or sexual topics

Plasma, a fluid consisting of highly charged particles, is the single most abundant state of matter in the universe, yet our understanding of its properties remains incomplete. One common method of generating plasma is by inducing a large voltage difference between two charged electrodes in a low-pressure environment, referred to as direct current (DC) plasma. Understanding the relationship between plasma temperature and spectral line intensity as a function of external parameters, such as voltage, pressure, and position, is crucial to optimizing plasma-based processes. This study analyzes these dependencies systematically to help build a further understanding of the spatially dependent properties of DC plasmas. We extract electron temperature from spectroscopic measurements by analyzing line intensities assuming a Maxwell-Boltzmann electron energy distribution. The intensity of spectral lines is related to electron energy via the Boltzmann factor, allowing for temperature determination through a logarithmic plot of intensity ratios versus upper energy levels. By varying voltage and pressure, we identified trends in intensity and temperature, providing insights into plasma behavior. Our results suggest that higher discharge voltages correspond to an increase in electron temperatures, indicating a direct relationship between voltage and temperature. These results provide a greater understanding of plasma-based processes, paving a path toward greater efficiency in applications such as semiconductor manufacturing, surface treatment, and materials processing.

Human Rhinovirus (HRV) is one of the primary causes of mild upper respiratory infections and is the most common infectious agent which affects billions of humans globally. To most healthy individuals, this illness causes mild symptoms. However, in populations who have immunosuppression, comorbidities, or predisposition health issues, this virus can cause severe symptoms which can lead to possible hospitalizations and even an increased mortality rate. Given the lack of approved therapeutics for this disease, our project aims to prepare a target Phenylpropenoid, which is an organic molecule that has been previously isolated from the plant Bupleurum fruticosum and has reported antiviral qualities against HRV. Our synthetic approach toward the target compound involves a three-stage process: synthesizing a phenylpropenol fragment, preparing a bis-enoate fragment, and combining the two through esterification to access the target phenylpropenoid. We have successfully prepared the phenylpropenol fragment and are working toward accessing the bis-enoate fragment for examination in the final esterification.  Our findings will enable preparation of derivatives to assess in bioactivity studies that may provide valuable insights for future target design.

This investigation is based on the famous intermediate axis theorem, often called the tennis racket theorem. This theorem describes why objects with three distinct moments of inertia, around three different axes, have an unstable rotation around the intermediate axis (the axis with the intermediate moment of inertia) while the axes that have the largest and smallest moment of inertia have a stable rotation. This phenomenon can be observed in rotations of everyday objects like tennis rackets and phones. By videotaping rotations of different objects with three distinct moments of inertia around three axes, and visually examining the intermediate axis, one can notice the instability of the intermediate axis compared to the stability of rotations about the other two axes. We mathematically analyzed the motion around three axes using Euler’s equations of rotations, the equations governing the dynamics of a rigid body undergoing rotational motion. We solved the differential equations demonstrating the instability around the axis with the intermediate moment of inertia. This behavior was also simulated in MATLAB using Euler’s equations of rotations. Our graphs of velocity as a function of time for rotation around the three axes, demonstrated and justified the visual observations from the videos. These experimental and computational approaches can lead students to a comprehensive understanding of the intermediate axis theorem.

Formalization is the process of translating human-written mathematical proofs into a form that can be verified by a computer. A popular tool for this is Lean, a proof assistant that represents proofs as code. However, the process of formalizing proofs in Lean can be slow and time-consuming. Our research explores so-called "autoformalization" strategies, which aim to automate the generation of Lean proofs. We propose a tree-based search framework to formalize mathematical theorems in Lean using Language Models. This approach explores potential proof steps as branches in a tree, using AI models to suggest "tactics" at each node. This has the benefit of avoiding hallucinations by rigorously checking that AI suggestion represent valid Lean code. We employ both Large Language Models such as Claude Sonnet 3.5 and specialized fine-tuned Small Language Models such as Lean-Dojo. We use Pantograph to interact with Lean, leveraging its native support of Monte Carlo tree search. We assemble a small set of simple and medium-difficulty mathematical theorems to benchmark against, called nanoF2F. Additionally, we benchmark our system on the well-established miniF2F benchmark created by OpenAI.

Previous evidence points to the benefit of early literacy intervention and support for bilingual children. Therefore, the need for culturally responsive practices in the field of speech-language pathology is essential for the growing bilingual population across all settings. Although there is substantial literature on the home literacy environment (i.e., resources and practices that families use during book reading at home), most of the existing evidence comes from monolingual children. The purpose of our research is to analyze the important relationship between child and caregiver during shared book reading to understand parents' language use and its impact on child vocabulary and grammar. Our research questions are: 1) what is the amount of book reading reported by families; 2) how much bilingual input does the parent produce; and 3) how is this related to children's vocabulary and grammatical development? We collected videos of parent-child book reading in the home and we measured vocabulary development with a parent-report vocabulary checklist in English and Spanish. We also collected environmental surveys containing questions regarding the literacy environment (e.g., duration of book reading; how often they read; and what language they read in). We hypothesize that children who receive more bilingual input during book reading will demonstrate larger vocabularies and more complex syntax. As research assistants in the Child Language Lab, we score standardized language assessments and transcribe the book reading interactions. We have completed scoring and are in the process of analyzing the data from parent report instruments and the transcribed videos. This research may identify key factors in creating an enriching, supportive literacy and language environment for developing multilingual speakers. We can use the findings of this study in the field of Communication Sciences and Disorders and may improve interventions for bilingual children, especially for daycares and preschools. 

The University of Washington’s Center for Global Health Nursing (CGHN) promotes and advocates for the role of nursing in global health by expanding nursing research and providing educational opportunities to students that bridge global and local perspectives. The CGHN’s three research pillars encompass Global2Local, Innovative Methods, and HIV/AIDS. We aim to clarify the global health interests and priorities of UW School of Nursing (SoN) students and increase the visibility of the CGHN. By increasing the CGHN's visibility, our goal is to increase the number of students participating in study abroad, scholarship opportunities, related coursework, and research to further engagement upon graduation. We developed a 19-item survey through RedCAP to identify nursing students’ knowledge, attitudes, and experiences related to global health and the CGHN and administered it at baseline and end line (after six months). Students across all UW SoN programs participated. Baseline data allowed our team to identify areas of focus (study abroad, scholarships, research) and optimal modalities to deliver information (annual Go Global event with global health (GH) nursing speakers, new social media account to amplify opportunities, and pop-up events to bolster enthusiasm). The center’s targeted efforts to meet the dynamic interests of students and the impact of this were informed and documented by our surveys. Surveying the priorities of students and using that information to disseminate services and opportunities effectively helps contribute to a robust community of GH nursing students, researchers, and practitioners.

Fluoride intake is essential for dental health, yet excessive consumption can lead to fluorosis, a condition negatively affecting teeth and bones. Tea, one of the most widely consumed beverages globally, naturally accumulates fluoride, making it a significant but often overlooked dietary source. Black tea is the most popular type of tea consumed in the U.S. In this study we compared fluoride levels across six brands of black tea and investigated how brewing conditions and water sources affect fluoride concentrations in tea. We brewed black tea from six locally popular brands (Lipton, Tazo, Fortnum & Mason, Twinings, Tetly, and Harney & Sons), using two water sources (distilled water and Seattle tap water), with four samples for each brand using both water sources. We brewed 50 mL of water at 100°C, then we let each sample of the tea sit for 5, 10, and 20 minutes. Ion chromatography was used to measure fluoride concentrations at each time interval. We compared these values to the U.S. Environmental Protection Agency's (EPA) recommended fluoride level of 4.0 mg/L. Our results help characterize the variation between brands and the influence of brewing duration on fluoride release. These findings contribute to a better understanding of fluoride exposure from tea consumption, helping consumers make informed choices about their dietary fluoride intake.

Beaver dams can function as natural filters helping decrease pollution in streams, creeks, and rivers. Beaver dams slow down the water flow in a creek or river, forming ponds that help trap excessive nutrients. An excess of nutrients such as phosphate and nitrate can cause eutrophication, leading to increased algal blooms that can produce toxins and ultimately deplete oxygen in the water. This study investigates the ion levels of chloride, fluoride, phosphate, nitrate, sulfate, and bromide upstream and downstream of the major beaver dam at Pipers Creek in North Seattle's Carkeek Park over the course of a year to better understand the long-term impacts of the dam. We collected three water samples at each of eleven sites along the creek, eight upstream from the dam, and three downstream. Ion chromatography was used to measure the concentrations of anions at each site. The results of this study help elucidate the role of beavers in moderating water quality and provide important baseline data documenting seasonal variations in the nutrient load at Pipers Creek. These findings can also be used to better understand the impact of new beaver dams in other freshwater systems.

Low-income communities are often disproportionately exposed to air pollution. High concentrations of pollutants such as particulate matter under 2.5 µm (PM2.5) and human aerosol emissions, including carbon dioxide (CO2), have been linked to various health and cognitive issues. Performance arts, including singing and playing instruments, produce human aerosol emissions and are considered high risk for airborne disease transmission. Our study evaluated the accumulation of CO2 and PM2.5 in high-risk environments (band classrooms) in low-income public schools in King County (WA), to determine whether there is a correlation between accumulation rates and Title 1 designation. Title 1 designation, which provides government funding for schools with a high percentage of students from low-income households, was used to represent low-income communities. We compared four middle schools that qualified for Title 1 designation to one school that did not qualify. Concentrations of CO2 and PM2.5 were measured using the Aranet4 Home CO2 sensor and a PurpleAir Classic sensor for PM2.5. We took a baseline measurement of both concentrations when the classroom was unoccupied. We then analyzed the change in concentration rates when classes were in session, taking into account classroom size and number of students. Our data showed concentrations above recommended levels at 1,370 ppm (parts per million) for CO2 in one of the Title 1 schools suggesting that Title 1 schools may be at greater risk of poor indoor air quality, though additional studies are needed. This additional exposure to pollutants and human aerosol emissions in already high-risk environments like band classrooms may lead to increased airborne disease transmission, highlighting the disparity in healthy learning environments. These classrooms require additional measures to maintain healthy concentrations of CO2 and PM2.5 to reduce the risk of airborne disease transmission particularly in low-income communities. 

The balance of ions in soil and water directly impacts sustainable agriculture, human health, and livestock well-being. Small family farms, such as the one in this study, often depend on well water for household and agricultural use, making water quality essential for both food safety and long-term farm viability. This study investigates the spatial distribution of key anions, including nitrate (NO₃⁻), nitrite (NO₂⁻), and phosphate (PO₄³⁻), in soil and well water across a small family-operated farm in Woodinville, WA. These ions were selected due to their roles in plant growth, soil chemistry, and potential health effects on humans and animals. The farm sustains 68 animals, including chickens, cows, donkeys, alpacas, llamas, sheep, quails, and horses, and provides food and water for seven residents. Soil and water samples were collected from distinct zones, including livestock pens, vegetable fields, and tap water from the farm’s well, to evaluate how land use influences ion distribution. Soil samples were collected at multiple sites; ions were extracted from the samples using a  common water extraction method. Ion chromatography (IC) was employed to quantify anion concentrations and assess spatial variability. While this study does not determine definitive sources of the ions, analyzing variations in these ion concentrations near crop fields and livestock areas can help assess potential nutrient leaching and runoff. This type of comparative analysis of soil and well water samples helps quantify potential risks to both farm operations and the health of residents and livestock. This research underscores the importance of ongoing water and soil quality monitoring to ensure the sustainability of small-scale farms that rely on well water and homegrown food, while offering insights for improved land and resource management practices

All mammals experience a slowdown of cardiac pacemaker rate with aging. The main mechanisms to explain that phenomenon are related to alterations in the ionic currents that underlie the diastolic depolarization phase of the action potential. We have previously reported that pacemaker cells from old mice have reduced L-type calcium currents. We further explore the mechanism underlying that reduction, testing cell hypertrophy and alteration in the scaffolding of L-type calcium channels as potential mechanisms. To test for cell hypertrophy, we combined immunostaining and high-resolution imaging to map the HCN4-positive pacemaker region of isolated upper heart explants from young and old mice. We compared cell length, width, and area between young and old cells. We also determined these morphological parameters in HCN4-positive enzymatically dissociated pacemaker cells. We found no significant difference in cell dimensions or area between ages, ruling out hypertrophy as a potential mechanism. We used mass spectrometry to identify expression changes in scaffolding proteins essential for calcium channel organization at the plasma membrane. Through this approach, we identified a large reduction of caveolin 3 as a possible mechanism. Caveolin is a protein essential to forming signaling microdomains between calcium channels and other proteins. Using western blotting, we confirmed a 50% reduction of caveolin 3 in isolated pacemaker tissues from old animals. Using proximity ligation assay and super-resolution microscopy, we showed altered recruitment of L-type calcium channels into caveolae. Our findings suggest that the age-associated decrease of L-type calcium current is caused by a reduced insertion of these channels in caveolae.

The heart's primary function is to pump blood to supply oxygen and nutrients to the body. The biomechanical principles of the heart are determined by specializations at the organ, tissue, cellular, and molecular levels. Little is known about how these specializations have adapted to sustain high heart rates in animals with extreme biology, as is the case of the hummingbird, whose heart rate above 1000 bpm makes it the endotherm with the highest heart rate observed in nature. We hypothesize that the hummingbird heart has evolved several adaptations at all the abovementioned levels to i) generate fast firing rates, ii) optimize electrical-contraction coupling, and iii) sustain fast contraction-relaxation cycles. Using different histological and imaging approaches, we have started to characterize the architecture of the hummingbird’s heart for the first time in a research lab. To describe the overall dimensions and structure of the hummingbird heart, we generated CT scans and 3D reconstructions of iodine-labeled Calypte anna hummingbird hearts. To characterize the organization of the tissue, we present data using hematoxylin-eosin and lectin stainings in fixed paraffin-embedded slices of the hummingbird heart. Our preliminary results showed that hummingbird ventricles have a cell density of 110 cells per 5000 µm2, around 7-fold larger than mouse ventricles. Ventricular cells in the hummingbird are 8-fold smaller with a cross-sectional area of 41 ± 4 µm2. Hummingbird hearts also have a higher capillary density with 18.0 ± 0.6 capillaries per 2500 µm2. Our results provide a foundation for structural and functional characterization of the hummingbird heart at an organ, tissue, and cellular level while opening avenues for further investigation of extreme cardiac physiology.

Certain species exhibit the remarkable ability to regenerate their appendages, a process that requires complex metabolic pathways to facilitate the cellular proliferation needed to regrow tissue. Among these species, Xenopus tropicalis, the Tropical Clawed Frog, serves as a great model for regeneration studies because of its transient regenerative capacity. X. tropicalis tadpoles exhibit the ability to regenerate their tails, but this capability is gradually lost after metamorphosis. This unique characteristic allows for direct comparison of regenerative and non-regenerative processes within the same species. Previous work from the Wills lab indicates that genes encoding the enzymes of the pentose phosphate pathway (PPP), which generates precursors of biosynthetic molecules such as nucleotides and lipids, are highly expressed during tadpole tail regeneration. Although tail regeneration has been well studied, the variation in hind limb regenerative capacity across developmental stages and the metabolic pathways involved remains unclear. Hence, I performed a live imaging study to determine the developmental progression of hind limbs and assess their regenerative potential. This data suggests a decrease in success as the tadpole gets older. Immunohistochemistry staining of mitotic cells in developing limbs shows that proliferating cells decline as regeneration competency decreases. I hypothesized that genes for the PPP enzymes would also be expressed during successful limb regeneration, which was confirmed by in-situ hybridization. Together, these findings indicate that the regenerative capacity in limbs of X. tropicalis is stage-dependent and that PPP genes are expressed during all stages of regenerative capacity. This provides insights into the role of metabolic reprogramming in appendage regeneration, with the potential for translating it into non-regenerative species like mammals.

Stiffness measures derived from MR Elastography have shown value in guiding treatment decisions and monitoring effectiveness of therapies for liver disease but it requires extra hardware, longer scan duration and is susceptible to motion and breathing artifacts. Recent studies have revealed a strong linear correlation between water diffusion and tissue stiffness, demonstrating that Diffusion Weighted MRI (DWI) can be used to estimate stiffness values in liver tissue. DWI-derived stiffness values may help evaluate treatment-induced changes in breast cancer but to our knowledge, this has not yet been tested. The purpose of my ongoing study is to calibrate DWI estimates of tissue stiffness for the breast by optimizing DWI parameters (diffusion weightings, or ‘b-values’) and  calibration coefficients (a, b), evaluating the potential of stiffness measures for monitoring response to neoadjuvant chemotherapy (NAC) in breast cancer. We collected baseline and early treatment MRI exams from 25 patients undergoing NAC in this IRB approved study along with their treatment outcomes based on pathologic response post completion of NAC. I evaluated  the stiffness values obtained from different b-value pairs (low b-values: 100/200; high b-values: 800,1500,2000 s/mm²) and calibration coefficients(a,b=-9.7,13.9:-10.8,17.5:-8.8,21.2) and compared it to the invasive breast cancer stiffness values reported in literature. I also evaluated the performance of the optimized parameters to predict treatment response. The optimal b-value pairing (b=200,1500s/mm²) and coefficients a=-9.7,b=13.9 produced stiffness values consistent with literature. Using this approach, the performance for predicting treatment outcomes between responder and non-responder groups was AUC=0.84. These preliminary findings suggest that DWI based virtual elastography could serve as a non-invasive tool to assess tumor stiffness and track treatment efficacy, potentially improving breast cancer management.

Protein kinases have been found to regulate cellular processes such as growth and stress response. Thus, they act as excellent targets for drug treatment. The Mycobacterium tuberculosis (Mtb) genome encodes 11 serine/threonine protein kinases. Our lab has previously found that two of these kinases, PknF and PknL, show a large survival deficit when induced. They phosphorylate similarly throughout central carbon metabolism (CCM), a process known to be involved in cellular survival. To test kinase regulation of different pathways in CCM, I tested the growth of avirulent Mycobacterium tuberculosis (aMtb) strains expressing PknF or PknL using two different carbon sources: propionate and succinate. Propionate is broken down into propionyl-CoA, a toxic co-intermediate, which passes through the methylmalonyl or methylcitrate pathway to enter the citric acid cycle at succinate. The methylmalonyl pathway requires vitamin B12 to proceed and prevent toxic propionyl-CoA build up. Thus, propionate + B12 was tested to further elucidate regulation of these pathways. I measured colony-forming units (CFU) to quantify aMtb survival in these growth conditions. I compared survival measurements of the PknF and PknL induced strains relative to an empty vector control strain. I found that PknF induced grown with propionate showed a greater survival deficit by day 7 compared to the strain grown in succinate. Interestingly, the addition of B12 did not rescue growth as it did in the empty vector control. PknL induced grown with propionate shows a greater survival deficit compared to succinate; however, the addition of B12 decreased the survival deficit experienced in propionate. Due to this difference between B12 phenotypes, we hypothesize that PknF induction is regulating the methylmalonyl pathway, resulting in no rescue of the survival deficit. These findings can be used to inform future studies on PknF and PknL as potential targets for tuberculosis treatment during infection.

Antibiotic resistance is an increasingly critical concern for the treatment of bacterial infections, rendering new therapy options progressively more necessary. Gram positive bacteria are common infectious agents in skin and soft tissue infections, pneumonia, urinary tract infections, bacteremia, and more. A novel antibiotic candidate, MRS-2541 has been demonstrated to inhibit Gram positive methionyl-tRNA synthetase and decrease bacterial loads of both methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pyogenes in mouse thigh infections to the same degree as currently recommended therapy. This study aims to further characterize the activity of MRS-2541 against Gram positive bacteria including Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus lugdunensis, Staphylococcus saprophyticus, Staphylococcus aureus, MRSA, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus salivarius. I conducted this study by first determining the preliminary minimum inhibitory concentration of MRS-2541 in growth media against each of the aforementioned organisms. I then use these results to guide time kill assays that characterize MRS-2541’s synergy with another antibiotic often used to treat Gram positive infections outside of the United States. Preliminary results demonstrate that MRS-2541 inhibits the above-mentioned organisms. Synergy experiments with MRS-2541 and existing antibiotics will be performed and results will be presented at the symposium. These results will further define the spectrum of activity as well as synergy of MRS-2541, allowing new insight into its candidacy for clinical trials. As a novel antibiotic candidate, the development of MRS-2541 will help address the increase in antibiotic resistance among Gram positive bacterial infections.

Safe drinking water in schools is crucial for children's safety and academic performance. While Seattle Public Schools has tested for some contaminants, such as lead, the district's responsibility for ion-specific testing for anions such as phosphate, bromide, nitrite, nitrate, chloride, sulfate, and sulfite is less clear. High concentrations of anions pose potential health risks, including reduced oxygen in red blood cells, higher risks of tumors in children, and diarrhea. This research investigated the anion concentration in water fountains across seven high schools in the Seattle Public Schools. Twenty-one water samples were collected from seven public high schools and analyzed for anion concentration using ion chromatography. Results were compared to the Environmental Protection Agency's (EPA) maximum contaminant level (MCL). All test samples were below the EPA's MCL. These results suggest that the drinking water in these schools does not pose potential risks to students from anion contamination. While regular monitoring and management are still necessary to maintain safe drinking water, Seattle Public Schools have met the safety requirements for anion concentration in their drinking water. 

Obesity is linked to reproductive dysfunction through defects in the hypothalamic-pituitary-gonadal (HPG) axis that arise by unknown mechanisms. Importantly, rodents fed a high-fat diet (HFD) develop similar hypogonadism and reduced ovulatory capacity. During HFD feeding, CNS immune cells (microglia) become activated in the hypothalamus, promoting inflammation, and altering neuronal function indirectly and via cell-cell contacts. Surprisingly, however, genetic ablation of this microglial inflammatory response exacerbates rather than improves HFD-induced HPG axis dysfunction including altering the activity of hypothalamic neurons that express the key reproductive neuropeptide GnRH. Therefore, we hypothesized that increased microglial inflammatory signaling during HFD feeding helps maintain GnRH neuron integrity. To test this hypothesis, we used immunohistochemistry (IHC) to assess microglia-GnRH cell-cell interactions in the hypothalamus of 15-week HFD-fed female mice with microglia-specific deletion of IKKβ (IKKβ-MGKO), a critical regulator of the inflammatory NF-κB pathway. IHC studies using GnRH and Iba1 (microglial marker) revealed fewer cell-cell contacts between GnRH neurons and microglia in the preoptic area of the hypothalamus (POA) of IKKβ-MGKO mice compared with controls. In addition, we found that IKKβ-MGKO mice have reduced levels of Iba1 and total numbers of microglia but no changes in microglial cell morphology as determined by Sholl analysis. These findings suggest that HFD-induced microglial inflammatory signaling promote cell-cell interactions with GnRH neurons that may contribute to maintenance of HPG axis integrity and female reproductive function during diet-induced obesity.

Despite the development of effective COVID-19 vaccines, countries with high rates of HIV infection still have limited vaccine access and inadequate access to antiretroviral medications essential for controlling HIV. Studying COVID-19 vaccination in people living with HIV (PLWH) is needed to improve vaccination strategies in immunosuppressed populations. Previously, in pigtail macaques (PTM) we showed that COVID-19 repRNA vaccination elicits durable and protective immunity against SARS-CoV-2 infection. Here we utilized the simian immunodeficiency virus (SIV)-infected PTM model of HIV/AIDS to test the hypothesis that COVID-19 repRNA vaccination is less durable during immunosuppression. Nine PTM were enrolled into the SIV naive (n=4) and experimental SIV-infected (n=5) cohorts. SIV-infected PTM were infected with 10,000 units of SIVmac293M seven weeks prior to the first vaccination. All PTM were given 2-4 COVID-19 repRNA immunizations, encoding the SARS-CoV-2 WA.1 Spike protein, to reach maximal immunogenicity and monitored for 26 weeks for vaccine durability. Vaccine recall was evaluated by administering a booster immunization after immunity responses waned. Blood and bronchoalveolar lavage samples were collected every 2-4 weeks. SIV-infected animals were monitored for SIV disease progression, including measuring CD4 counts in peripheral blood. Enzyme-linked immunosorbent assays (ELISAs) were used to quantify longitudinal Spike-specific binding IgG antibodies. Preliminary data shows that COVID-19 repRNA vaccination elicited robust anti-Spike IgG antibodies in both PTM groups, with diminished responses in some animals within the SIV-infected group.  Anti-SARS-CoV-2 neutralizing antibodies were also generated in both groups and interestingly, more durable in SIV-infected animals. Ongoing analysis includes evaluation of IgM and IgA binding antibodies. Collectively, this study suggests SIV-associated immunosuppression impacts vaccine-induced humoral memory, which could, in turn, impact long-term protection from COVID-19. These findings are crucial for improving vaccine regimens for PLWH and other immunosuppressed individuals.

Viral evolution theory hypothesizes that specialist strategies increase fitness by reducing interspecific competition, while generalist viruses increase fitness by accessing multiple hosts. However, specialism may come at the cost of infecting few hosts, while generalism may reduce fitness in any single host. These tradeoffs have been demonstrated in Infectious hematopoietic necrosis virus (IHNV), an aquatic rhabdovirus infecting multiple salmonid species. High rates of viral replication have been observed for specialized subgroups in their respective hosts, while lower rates of replication across multiple hosts have been observed for the generalist subgroup. However, the host-virus mechanisms underlying these replicative differences are unknown. Here, I aim to characterize the early innate immune response of sockeye salmon, the ancestral host of IHNV, to specialist and generalist subgroups at target tissues. Specifically, I seek to test whether sockeye salmon display distinct transcriptomic responses to IHNV specialist and generalist subgroups in the kidney 2 days post-exposure (dpe). To accomplish this goal, RNA was extracted and sequenced from kidney tissue of individuals 2-dpe following exposure to specialist (n=9), generalist (n=9), or control (n=4) IHNV treatments. Overexpressed and underexpressed genes will be identified between each subgroup and control samples. These genes will then be used for pathway enrichment to compare differences in transcriptomic response. Replicative rates have shown a difference between specialist and generalist subgroups of IHNV 2-dpe in the kidney; therefore, we expect to observe differences in the number and magnitude of over- or underexpressed genes and enriched pathways between hosts exposed to specialist and generalist subgroups. Results from this study will aid in characterizing evolutionary mechanisms underlying viral specialism and generalism, understanding host innate immune response and evasion strategies, and identifying biological markers associated with response to viral exposure. This knowledge will be critical in predicting future disease outbreak and informing disease mitigation strategies.

Protein subunit vaccines are highly used today as an alternate vaccine platform to older vaccines such as live-attenuated viruses. They contain a protein antigen of the virus or bacterium that can be recognized and targeted by the immune system, and an adjuvant that amplifies the immune system response to this protein by widely putting the immune system on alert. The most commonly used adjuvants pose the risk of possible adverse reactions and are not created to target specific immune pathways, but rather stimulate general inflammation. To design a vaccine adjuvant that generates a more targeted immune response, we are using the self-assembling protein nanoparticle, I53-dn5, to display a CD40 binder that mimics the T Cell ligand, CD40L, by binding to B cell surface receptor CD40. We aim to create a particle that can replicate the binding interaction between B and T cells in the lymph node responsible for triggering antibody maturation, and B cell proliferation and differentiation. We hypothesize that this multivalent display of CD40 binder will generate potent B cell responses allowing us to respond to an antigen more effectively than current adjuvants. We are utilizing computational protein design methods like RFDiffusion, ProteinMPNN, and AlphaFold2 to optimize this display, and testing these designs in vitro for stability and ability to elicit downstream signaling effects of the CD40/CD40L interaction. This research holds two promising innovation potentials. The first is creating higher potency adjuvants by stimulating specific signaling pathways for use with protein subunit vaccines. Secondly, these materials can be used as a more stable and potent molecule in biochemical assays such as being an alternative to feeder cell lines in B cell support culture.

Over a hundred years after the Spanish Flu, the influenza A virus (IAV) remains a leading cause of respiratory infections and mortality worldwide. The proliferation of IAV causes many of the symptoms associated with IAV clinical disease. However, the severity of acute lung injury (ALI) from IAV is primarily driven by the host's immune response to infection. The mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated protein kinase (ERK) signaling cascade is a highly conserved pathway that is activated during lung injury and inflammation in both rodents and humans. Two MEK isoforms, MEK1 (Map2k1) and MEK2 (Map2k2), activate downstream effectors, ERK1 and ERK2, and control critical cellular processes, including the intensity and duration of inflammatory signaling. Our prior research revealed that MEK2-deficient mice exhibited improved weight recovery and overall fitness during IAV infection, suggesting that MEK2 is a host response exacerbating ALI during IAV infection. During IAV infection, excessive pro-inflammatory cytokine production drives immune cell recruitment into the lungs, leading to collateral tissue damage that impairs organ function and exacerbates disease. We hypothesize that MEK2 enhances immune cell recruitment to the lungs, enhancing inflammation, which may occur through exuberant chemokine signaling. To investigate this, we infected MEK2-deficient and wild-type mice with mouse-adapted IAV (H1N1, PR8) and collected cells from bronchoalveolar lavage (BAL) and lung homogenates. Using flow cytometry, we found reduced immune cell recruitment, including decreased numbers of monocytes, dendritic cells, monocyte-macrophages, CD4+ T-cells, CD8+ T-cells, and B-cells. Next, we assessed levels of key chemokines known to attract monocytes and lymphocytes by measuring their gene expression in the lungs and protein levels in the BAL. Investigating MEK2’s impact on chemokine signaling will elucidate the mechanism by which MEK2 perpetuates lung inflammation and injury during IAV infection and will guide the development of future host-directed therapies for IAV-induced lung damage.

Transcriptional repression plays a critical role in the regulation of various biological processes, including developmental pathways and disease progression. Corepressors are proteins recruited by partner proteins to negatively influence the transcription of genes. TPL is a corepressor from the model plant Arabidopsis thaliana, and is known to play a pivotal role in transcriptional repression. My project aims to identify other proteins that work with TPL to form a transcriptional repression complex at a single engineered locus. To further understand the function of corepressors, we built a synthetic repressor system, dCas9-TPL, designed to specifically repress the transcription of the RUBY reporter gene. When expressed, the RUBY reporter turns Arabidopsis thaliana pink. In previous phases of this research, we utilized the EMS (ethyl methanesulfonate) mutagenesis protocol to create a population of plants containing many random mutations. Screening these plants for increased RUBY expression, I successfully Identified promising homozygous lines where plants demonstrated bright pink flowers and unique phenotypes such as early flowering, light avoidance, and small stature. Last quarter, I sent five lines to be sequenced and each line displayed distinct mutations that I can further explore to pinpoint the exact TPL interactor responsible for its unique phenotype. I am also investigating known TPL interactors such as SPT4, SPT5, and MED21 by creating transgenic lines within my control dCas9-TPL + RUBY line. Through genetic screening, I have validated the phenotypes among these control experiments. By investigating the intricate network of interactions between these regulatory proteins, I aim to gain a deeper understanding of how gene expression is coordinated across different cell types and how this process controls complex developmental pathways.

The timing of flowering in Arabidopsis thaliana is tightly regulated by environmental cues that induce the expression of FLOWERING LOCUS T (FT), a mobile signal responsible for floral induction. Recent studies have identified FPF1-LIKE PROTEIN 1 (FLP1), a gene co-expressed with FT in phloem companion cells, as a potential regulator of flowering. Given FLP1’s genetic similarity to known flowering regulators, we hypothesize that it functions as a mobile flowering-promoting signal. Using predictive protein interaction modeling with AlphaFold 3, followed by Bimolecular Fluorescence Complementation (BiFC) and Yeast-Two Hybrid assays, we confirmed that FLP1 interacts with key proteins in the shoot apical meristem. Overexpression of FLP1 leads to early flowering in Arabidopsis, while loss-of-function mutants exhibit delayed flowering, supporting its role in floral induction. Interestingly, while FLP1 homologs generally promote flowering across species, a contrasting effect in Brachypodium distachyon has been observed, where overexpression of its homolog (BdFLP1/BdFLP7) delays flowering. This unexpected result raises critical questions about the molecular basis of functional divergence among FLP1 homologs. To investigate this, we are introducing BdFLP1 and BdFLP7 into Arabidopsis to assess their effects on flowering time and to determine whether structural differences or distinct protein interactions underlie their divergent functions. Through molecular cloning, transgenic expression analysis, and biochemical assays including western blotting, immunoprecipitation, and mass spectrometry, we aim to elucidate the role of FLP1 and its homologs in flowering regulation. Understanding these mechanisms will provide deeper insights into conserved and species-specific pathways controlling floral induction. This knowledge is essential for improving crop adaptation strategies in the face of climate change, highlighting the broader significance of our research in plant developmental biology.

Plants' defense mechanism against herbivory is integral to both resistance in nature and the global food supply. Glycine max or soybean, is one of the most widely grown crops in the world, and suffers substantial losses from pests, including many Lepidopteran species. Related legumes, including cowpea, and common bean, can respond to Lepidopteran herbivory by detecting Inceptin-11 (In11), a short peptide found in larval oral secretions. The protein responsible for this ability, Inceptin Receptor (INR), is not found in soybean. The aims of this project are two fold, firstly introducing INR into soybean lines and testing for improved resistance to Lepidopteran herbivory, and secondly studying the effects of INR on defense gene expression in soybean, in order to better understand mechanisms of herbivory resistance. The first step in this project was to create soybean lines which consistently express INR. This was done by sending our INR construct to collaborators, who used it to inoculate multiple soybean lines, then breeding the corresponding lines until response to In11 was seen in all offspring. We will then test larval beet armyworms (Spodoptera exigua) on both INR- and INR+ lines. We expect the INR+ lines to have significantly lower S. exigua growth, indicating an improved immune response. We are also infiltrating INR- and INR+ lines with both In11 and flg22 (a well studied bacterial elicitor) for RNA sequencing of the early immune response. We expect genes involved specifically anti herbivory mechanisms being upregulated when compared to flg22. These two prongs allow us not just to demonstrate the viability of stable transgenic herbivory resistant lines, but to uncover the molecular mechanisms involved in that resistance, allowing for future scientists to better engineer the next wave of pest resistant crops.

According to the CDC report in 2022, Indigenous women experience 58% of intimate partner violence cases, which is one of the primary causes of homicide. The Reauthorization of the Violence Against Women Act (VAWA) has been credited for expanding protections for Indigenous women. This included increasing the provision of crimes under Tribal Jurisdiction and creating a pilot program for Alaskan Natives to prosecute non-Native offenders in villages. However, this policy reveals a gap between written law and people's experiences. This study examines the effectiveness of VAWA strategically, what demands were left out, and what those gaps represent in demanding changes through intersectional advocacy. In this qualitative research, I created a codebook to analyze the VAWA Congressional hearings from 2009 to 2022 to track the evolution of policy reforms from Indigenous activists. Applying a high-level textualized analysis by gathering a literature review, I utilized the framework of intersectional advocacy, which identifies the extent to which laws and interventions can create meaningful linkages across issues experienced by multiple marginalized people. VAWA remains to be a product of limitations in representation and holistic change to advance the needs of Indigenous people. Expected findings suggest that future policy reforms move beyond analyzing the issue through the lens of individuals to a community-based perspective. Intersectional frameworks will become a cornerstone of future policy work by propelling conversations centered around restorative well-being and healing. Creating bridges between people's lived experiences and legal institutions is foundational to creating critical correspondence. 

This research project explores relationships between queer activist organizations and the business community in Portland, Oregon, during the early 1990s. By examining the fight against Ballot Measure 9, which would have curtailed LGBT rights in Oregon if it had passed, this paper shows how queer activism was shaped and developed during the late 20th century, by both internal and external concerns. As they led the charge against Ballot Measure 9, queer organizations in Portland actively sought to engage businesses for their monetary support and tacit endorsement of LGBT rights. By comparing and contrasting the experiences of one queer organization that was developed specifically for this fight and one that had long-standing grassroots ties, this paper illuminates the scope and variety of queer-business connections. My focus on the opposition movement to Measure 9, composed of queer organizations and their business allies, also demonstrates the critical nature of these alliances to the political success of queer organizations, starting in the 1990s, with an impact reaching well beyond the specific context of this specific ballot measure. This project, centered around extensive archival research that was supported by Pacific Lutheran University’s Benson Summer Research Fellowship, offers a new layer of understanding to American queer activism during this period, with implications that still shape current-day affairs in both the U.S. queer community and the U.S. business community.

Substance use disorder disproportionately affects sexual and gender minority (SGM) youth compared to their heterosexual and cisgender peers, a disparity which is driven by unique stressors and systemic inequities. This systematic review synthesizes 122 empirical studies to explore the factors contributing to elevated rates of substance use among SGM youth and to identify gaps in existing prevention and intervention efforts. Findings reveal significant disparities, with SGM youth experiencing heightened vulnerability due to stressors such as expectations of rejection, interpersonal and structural discrimination, familial rejection, and other challenges of navigating a heteronormative world. These challenges are compounded by individual-level covariates including race, ethnicity, and socioeconomic status, which are often overlooked in existing research. A key finding is the paradox of community. While SGM-affirming spaces provide essential support, they are often closely associated with substance use. Despite sparse availability of targeted interventions, existing studies underscore the necessity of culturally relevant affirming approaches that address the unique needs of this population. Recommendations for youth, schools, practitioners, and families are provided, emphasizing the importance of fostering inclusive environments, reducing stigma, and building pathways to resilience and mental health. This review highlights an urgent call to action to address these disparities through innovative and inclusive prevention and intervention strategies.  

Autism is a neurodevelopmental condition characterized by social-communication differences and restricted, repetitive behaviors (American Psychological Association, 2013). While racial disparities in autism prevalence have been documented, not much research has examined how these differences appear in autism screening measures. This study investigates racial differences in Autism Spectrum Quotient (AQ) scores among non-autistic Asian and White adults to assess potential biases in autism screening. Using data from three NIH-funded studies (COBRA, BEAM, and The Korean Study), AQ scores from 166 participants (n=102 White, n=64 Asian) will be analyzed through t-tests and Repeated Measures Analysis of Variance (ANOVA) to compare total and subscale scores. Preliminary observation suggests that non-autistic Asian participants may be more likely to score higher on the AQ, raising concerns about false positives in autism screenings. Understanding these differences will help improve diagnostic accuracy, reduce disparities, and promote equitable access to neurodevelopmental resources.

How do we move beyond basic aid to truly support the mental well-being of displaced communities? Jordan, a growing nation in the Middle East, is globally recognized as a leading host for refugees. During my five-week Fall 2023 internship at the Institute for Family Health (IFH) in Jordan, I conducted a research project exploring how mental health and psychosocial support (MHPSS) programs address the needs of refugees and vulnerable populations, to fulfill requirements of my program on Psychology, Mental Health, and Well-being in Conflict-Affected Contexts. I employed participatory observation, analysis of material culture, and formal interviews to gather data. At IFH, I worked in both clinical and administrative settings, gaining firsthand insight into a healthcare model that prioritizes accessibility by ensuring high-quality mental health services regardless of wealth or citizenship status. I examined IFH’s use of the Inter-Agency Standing Committee (IASC) intervention pyramid, which balances specialized and community-based care to bridge gaps in mental health services. Through my research, I found that the most common mental health complaints are anxiety, depression, and PTSD. To address these complaints effectively, my research suggests that transformative care requires a holistic approach to MHPSS programs—integrating mental health practices, promoting illness prevention, building strong community bonds, and empowering future generations. This experience reshaped my understanding of global mental health challenges and led me to explore key questions, such as how organizations can expand MHPSS programs to meet growing demand and what role cultural and systemic factors play in shaping mental health interventions. My findings suggest that expanding MHPSS programs requires both increased resources and culturally responsive strategies. By sharing insights from Jordan, I aim to highlight scalable approaches and contribute to ongoing conversations about sustainable mental health interventions for displaced populations.

Asian Americans are victims of anti-Asian racism, but recent studies have also shown that they have a different role in perpetuating anti-Blackness and White supremacy. Our research aimed to specifically examine whether White and Asian Americans perceive a difference between anti-Blackness and White supremacy. We ran a qualitative study where anti-Blackness and White supremacy were defined for Asian and White American participants, who were then asked to write about their racial group’s relationship with those phenomena. We defined anti-Blackness as the belief that Black people are inherently inferior to others, and the corresponding practice of them being given insufficient power. Similarly, we defined White supremacy as the belief that White people are inherently superior to others and the corresponding practice of them being given disproportionate power. A few research assistants and I rated the similarity between the responses on anti-Blackness and White supremacy on a Likert scale from 1 to 7, with 1 indicating “not similar at all,” and 7 indicating “very similar.” We then performed a two-sample t-test (a type of statistical data analysis in psychological research) on this data to compare the responses between the Asian and White American participants. As expected, we found that the Asian American participants rated anti-Blackness and White supremacy as being more distinct than the White Americans did. The p-value for this data analysis was a statistically significant 0.004. These findings establish a foundation for future studies on the Asian American role in anti-Blackness and White supremacy. I have also conducted data analysis and ran participants for two such studies, which examined whether reminders of anti-Blackness caused Asian Americans to take more responsibility for anti-Blackness and show more solidarity with African Americans more than reminders of White supremacy.

Eating disorders increase the risk of co-occurring mental illnesses, such as depression and anxiety. Asian Americans are an underrepresented population in eating pathology research; they may be under or misdiagnosed and often do not seek services because interventions do not align with their culturally specific needs. The existing literature often neglects the impact of acculturation and acculturative stress on disease presentation and etiology. Acculturative stress arises from balancing the dominant culture's values with one's culture of origin, leading to psychological distress and disordered eating as a coping mechanism. Acculturation, the process of culture change, can increase the pressure to conform to Western thin beauty standards. People who ruminate may be particularly at risk for using disordered eating as a maladaptive coping mechanism against stress. Examining the critical roles of acculturation, bicultural stress, and rumination as unique and interactive determinants of eating pathology can lead to culturally relevant knowledge about its etiology and enhance utility and effectiveness of interventions. This study is aimed to examine acculturation orientations and bicultural stress as predictors of eating pathology symptoms, and rumination as a moderator. We hypothesize that higher levels of acculturative stress will be linked to greater eating pathology symptoms, over and above acculturation orientations. Rumination—particularly brooding—is expected to exacerbate the association between eating pathology symptoms and acculturative stress. Data are from the baseline measurement occasion of an existing longitudinal survey study that examined associations among mental health, personal and sociocultural risk and protective factors. Asian American undergraduate students (N=313; Mage=19.89; 72.5% U.S.-born; 55.6% female and 32.9% male) completed the baseline survey. With the anticipated support of the Mary Gates Scholarship, we will complete hierarchical regression analyses to test the hypotheses. Regression coefficients and effect sizes, model statistics, and p-values will be reported. 

First-generation college students (FGCS), those first in their families to pursue or complete a college degree, are a widely studied demographic across psychological research. However, much of the literature on FGCS examines their mental health and life experiences through a deficit framework, focused on systemic obstacles to success and categorizing students as “at risk”. Additionally, some research fails to recognize the importance of intersectionality, viewing FGCS’s mental health as separate from its systemic, social, and institutional contexts. To better highlight the assets and intersecting identities of FGCS, this strengths-based presentation explores existing literature about their mental health experiences, describes their risk and protective factors in developing mental health symptoms and conditions, and proposes mental health initiatives for FGCS and, specifically for, Latine FGCS. I use insights from interviews with Latine FGCS as illustrative examples to further demonstrate the importance of considering context and intersectionality in this area of psychological research.

Overgeneral Autobiographical Memory (OGM) is a common symptom of depression and Post-Traumatic Stress Disorder (PTSD). Instead of remembering specific details, individuals with OGM can only describe past events from their lives in general terms. The "trauma hypothesis" suggests that OGM emerges because individuals suffering from PTSD tend to reduce the number of details they retrieve about their memories to avoid remembering their trauma. However, this hypothesis does not fully explain how this avoidance is learned, or why avoidance spreads from traumatic memories to all autobiographical memories. To this end, we propose a computational model of OGM that integrates theories of memory retrieval and trauma with reinforcement learning. In this model, multiple episodic memories are nodes in an interconnected network, and memories are retrieved when visiting that node in the network. The more nodes that are visited, the more detailed that autobiographical recall will be. On the other hand, visiting more nodes comes with an increased risk of encountering a traumatic memory, which comes with negative emotional valence. The decisions about whether to visit another node or terminate the retrieval process are made using reinforcement learning, which takes actions based on predicted outcomes. By obtaining a greater understanding of OGM through this model, we hope to improve treatments for PTSD that specifically targets its effects on memory. 

The King County Brightwater Treatment Plant includes a marine outfall pipe anchored to the seafloor that discharges highly treated effluent from the Seattle metropolitan area into Puget Sound, Washington. Since 2009, as part of an eelgrass survey study, King County biologists have collected annual video footage of the outfall pipes from which they witnessed the abundance of organisms colonizing the pipe at all depths. Consequently, in 2012, King County biologists launched a ten-year project assessing the effectiveness of the high-density polyethylene (HDPE) outfall pipe at providing habitat for marine organisms and the composition of organisms it houses. Using a  remotely operated vehicle (ROV), they placed thirty plates of HDPE material adjacent to the outfall pipe at 100ft, 300ft and 600ft depths. Sets of replicate plates were then retrieved after 2, 5, and 10 years of deployment, at which time King County staff immediately took photos of each plate for analytical assessment. In this study, we analyzed the photos for percent live cover and composition of marine organisms inhabiting the pipe material, all across depths and time intervals. We hypothesized that the wastewater outfall pipe can function as a habitat; and the extent to which different organisms, their identifications and abundance, likely vary by depths due to the environmental conditions at different levels of depths. We found that percent live cover increased over time but did not vary across depths, and that certain phyla consistently dominated cover on the plates but dominant groups varied across depths. These findings allow experts in the field to consider using outfall pipes to provide additional habitats for marine organisms, and to assess communities of organisms at depths that are less accessible. 

Harmful algal blooms (HABs) are threats to a number of species in marine environments. One hypothesis states that excess nutrients in water lead to accumulations of certain plankton species that produce toxins. This can explain some illnesses such as paralytic shellfish syndrome in humans who consume impacted shellfish. HABs can be identified directly, but given the delays involved in analyzing results, other indicators may be used to predict presence of HABs as well. Possession Sound is an inlet of the Puget Sound located between Whidbey Island and the coasts of Everett and Mukilteo, Washington, connecting to the Snohomish River, as well as Saratoga Passage and Port Susan to its North and the main Puget Sound basin to its South.  Since HABs can occur in freshwater and saltwater for different reasons, Possession Sound’s status as a salt-wedge estuary makes it notable as a study site. To investigate the nature of HABs in Possession Sound, I analyzed plankton density data, chlorophyll-a levels, and phosphorus concentration data I collected in 2024 as well as data collected by the Ocean Research College Academy from 2016-2024. Chlorophyll-a concentrations were measured with a YSI EXO Sonde. Phosphorus concentrations of water samples were collected using a Niskin bottle and measured by the University of Washington Marine Chemistry Lab. I analyzed the progression of each parameter temporally and spatially. I expect to see clear spikes in certain plankton species, especially dinoflagellates, that align with similar-timed chlorophyll-a and phosphorus spikes. However, I predict that trends will be the least prominent in phosphorus concentrations due to its greater prevalence in freshwater than in saltwater. Understanding which plankton species are most responsible for HABs and temporal alignment of potential drivers can allow for better prediction of HABs in Possession Sound.

Zostera marina (eelgrass) is one of the many important biological features of Possession Sound, acting as a substrate for many microorganisms, a filter of greenhouse gases, and as protection for many species. The Possession Sound has been marked as a Seagrass Sanctuary by the Department of Natural Resources, which protects and monitors nearshore eelgrasses within the basin. By looking at what kinds of species are found in a marine environment, researchers can assess an ecosystem's overall health. Environmental DNA (eDNA) is a data capture technique used by researchers that picks up DNA traces left behind by organisms, and shows their presence/absence in a given area. The study site, Mount Baker Terminal, lies inside the Possession Sound basin near Everett, Washington, and contains a large eelgrass bed. I collected 10 samples using passive filters submerged at various depths inside and outside the eelgrass bed in 2024 and processed at a WDFW lab. I analyzed these data and 40 additional samples collected by the Ocean Research College Academy from 2021-2024 using similar methods. I hypothesized that there would be more species such as crustaceans, fish, and other plants inside the eelgrass because of its ability to protect and maintain a nutrient-dense environment. These data will help shed light on species richness in each environment, which has potential implications for understanding the overall health of the ecosystem and the critical role eelgrass plays in the estuary.

Possession Sound, located between the city of Everett and Whidbey Island, is a part of both a key economic area and a bustling marine environment. Because of the marine activity, scientists study all sorts of parameters involving the water including noise. Numerous studies have assessed ambient noise in marine environments to investigate the influence of tidal forces on ambient noise. These reports found that tidal noise or “flow noise” is observed around the 0-100Hz range with the most significant impacts observed centered around 25hz. The Ocean Research College Academy operates a SoundTrap ST400 STD hydrophone mounted to Mount Baker Terminal that takes recordings daily for most of the year. Mount Baker Terminal is a small marine terminal operated by the Port of Everett, located just north of the town of Mukilteo. Using data collected from the hydrophone, I took measurements of ambient noise in root mean square amplitude centered around the 25hz range and compared that to NOAA tidal data at Everett, Washington. Using these data I investigated the potential presence of a relationship between the tides and ambient noise. When the initial measurements of root mean square amplitude were compared to tidal data from the area the results showed that tides had no significant impact on the ambient noise at Mount Baker Terminal. Investigating the effects of tides on ambient noise can be crucial to future acoustic research done by researchers in the area as results could be affected by noise created or affected by tides. Future analysis should investigate the impacts of other natural contributors to the soundscape such as rain and wind.

The Eastern North Pacific gray whales (Eschrichtius robustus) have a long migration from their breeding grounds in Mexico to their feeding grounds in Alaska. A subgroup of the Eastern North Pacific stock, nicknamed the Sounders, deviate from the migratory path most gray whales follow to feed in the Salish Sea, typically between the months of March and May. Other studies show that gray whales feed on benthic organisms such as ghost shrimp. Studies conducted in the Arctic area of the gray whale migration route have seen sea ice playing an important role in the gray whales being able to enter the areas where they feed. One working hypothesis is that gray whale shifts in migration patterns are the direct result of climate change; this could explain why some of the Eastern North Pacific gray whales enter and feed in Possession Sound. I analyzed sightings data, shared by the Whale Museum and recorded in Possession Sound, WA from 2000-2022. These data, most of which were compiled by the Orca Network, were filtered to identify the number of visitations each month over the study period. Early analysis shows a phenological shift in the time of the gray whale's arrival and departure from Possession Sound. The shift shows an increase in the number of months gray whales are present in Possession Sound, from a March to May visit to a year-round presence. Although these results cannot explain the reason for the phenological shift, future research must look into related shifts in the Arctic ice formation as well as ambient air and water temperature shifts. Future research calculating density of ghost shrimp in Possession Sound will also indicate why this location is favored.

Ocean acidification is the reduction of pH in seawater due to increased carbon dioxide from fossil fuels in the atmosphere and other anthropogenic factors. Ocean acidification causes shellfish such as oysters to experience difficulty building their shells. Acidification trends in the North Pacific Basin are well documented, yet pH trends in Possession Sound, a salt-wedge estuary located in the Salish Sea is less documented. Possession Sound receives discharge from the Snohomish River and has human activity along the shoreline. In this study, the average change of pH in the middle of the North Pacific Ocean was measured and compared to the average change of pH in Possession Sound since 2016. I analyzed data collected from ARGOS Floats located in the central North Pacific Ocean. For Possession Sound, I used data collected from a  YSI EXO Sonde in partnership with the Ocean Research College Academy (ORCA). I collected data on 12 research cruises in 2024. I expect to find a slightly greater decrease in pH within Possession Sound than the North Pacific Basin due to the additional anthropogenic factors present in the Sound. Preliminary analysis shows a slight seasonal change in pH in Possession Sound, but little to no change yearly. I expect the data to show a steady decrease in pH for Possession Sound and the North Pacific Ocean basin every year since 2016. Calculating acidification rates and learning how they differ in various geographical locations, with separate factors, will increase understanding of the impacts of ocean acidification, which may be used in conservation efforts. 

A physiological response to acute stress, called anxiety, is thought to be an adaptive feature that allows us to adjust our behavior to better approach the situation causing stress. However, in anxiety disorders this response is maladaptive, leading to excessive anxiety. A key neural circuit is the projection from the locus coeruleus (LC) to the basolateral amygdala (BLA), and activation of this circuit produces anxiety-like behavior. However, little is known about how this alters the activity of BLA neurons. My Mary Gates research project seeks to utilize machine learning to understand how neuromodulatory input from the LC to the BLA alters the correlated activity of BLA neurons and their encoding of anxiety-like behavior. Mice expressing the excitatory opsin ChrimsonR in the LC and the calcium indicator GCaMP6s in the BLA received tonic (5hz) stimulation of LC terminals within the BLA through a GRIN lens to mimic stress-like release of norepinephrine into the BLA. LC terminals were stimulated while recording individual BLA neuron activity during a conflict-based test of anxiety-like behavior, the Elevated Zero Maze (EZM). To evaluate the correlated activity of BLA neurons as a function of stimulation, I used caGraph, a Python package that utilizes graph theory approaches to test the correlation of neurons from calcium imaging data. I investigated how stimulation affects graph theory communities (densely connected clusters) and clustering coefficients (strength of clustering) and found that stimulation causes an increase in the clustering of BLA neurons. To test the functional consequence of these ensemble shifts, I am using classification algorithms to assess the population encoding of the BLA neurons. I expect that stimulation of the LC terminals will increase the encoding of anxiety-like behavior. The findings of this project deepen our understanding of how the LC-BLA circuit mediates anxiety-like behavior, and may uncover novel treatment strategies.

Dopaminergic signaling within the striatum plays a crucial role in modulating reward and aversion, shaping behaviors such as food-seeking and consumption. While striatal dopamine release has been implicated in reinforcement learning and decision-making, the spatial and temporal dynamics of dopaminergic activity along the anterior-posterior axis of the striatum during consummatory behavior remain poorly understood. We investigated the role of dopamine in the striatum during the consumption of multiple solutions by employing a trial-based multi-spout behavioral paradigm with head fixed mice. To record the dopamine activity in the ventral and dorsal striatum, we utilized multi-site fiber photometry to record the fluorescent biosensor GRAB-DA2m along the anterior-posterior axis. Food restricted mice were given varying concentrations of sucrose as rewarding stimuli, while water restricted mice were given varying concentrations of sodium chloride as aversive stimuli. Our results revealed that dopamine responses scaled more across concentrations in the anterior regions of the striatum compared to the posterior regions. Additionally, we found more distinction between dopamine responses for the various concentrations of the aversive solution compared to the rewarding solution. Lastly, posterior striatal dopamine responses had a more rapid onset upon stimulus consumption, whereas anterior regions exhibited delayed responses, highlighting region-specific temporal differences in dopaminergic encoding. These findings refine our understanding of dopaminergic circuitry within the striatum and how dopamine-mediated responses to rewarding and aversive stimuli regulate feeding behaviors. By exploring this pathway, we offer potential insights into the mechanisms underlying disorders characterized by dysregulated reward including eating disorders and obesity.    

The locus coeruleus (LC) is a major neuromodulator source with widespread projections to distinct functional targets that influence arousal, anxiety, learning, and other behavioral states. Our lab has previously shown LC excitation triggers the release of norepinephrine (NE) into the basolateral amygdala (BLA). Recent studies suggest LC terminal stimulation may release DA into the dorsal hippocampus (dCA1) enhancing novelty-associated spatial learning. Our recent data show LC stimulation evokes DA release. Previously, release across regions, paradigms, and behaviors typically associated with LC have not been characterized, due to difficulty in separating DA from NE using traditional sensing methods. Due to this, the relationship between the LC and other DA systems remains unclear. To understand the mechanisms by which the LC may release DA independently of the ventral tegmental area (VTA), a major DA source, we have employed optogenetic stimulation to evoke release from neuron terminals and quantify the release dynamics of NE and DA. We used fluorescent biosensors to detect NE and DA, captured by a fiber optic cable and amplified to observe the relative dynamics of DA release. These sensors have tuned affinity and selectivity for NE and DA and use fluorescence as a proxy for neuromodulator release. In this project, we aim to elucidate how and under what conditions the LC is releasing DA across regions with different functions during aversive and appetitive behaviors. These data will enhance our understanding of the LC neuromodulator signaling that can become maladaptive and afflict anxiety, addiction, and more, and also demonstrate that the release of DA from the LC is dependent on the behavior induced.

The ability to pattern three-dimensional microscale cultures opens new avenues for examining the effect of nonplanar mechanical environments on mammalian cells and tissues. Our lab has developed a method for generating suspended tissues with spatial control using open microfluidic principles called Suspended Tissue Open Microfluidic Patterning, or STOMP. STOMP utilizes spontaneous capillary flow and capillary pinning to pattern suspended, multi-region tissues. Using similar microfluidic principles as STOMP, we have developed a method to pattern large (cm-scale) models via semi-open microfluidic channels called Suspended Nonplanar and Planar, or SNaP, geometries. I design these devices with computer-aided design, fabricate components on stereolithography 3D printers, pattern devices with standard pipettes, and culture resulting tissues for short- and long-term time periods to model biological scenarios. With the broad statement that human tissue is generally nonplanar in mind, my research focuses on three different geometries of tissue, 1) a sinusoidal wave, 2) a transwell-like mogul, and 3) a multi-region dome, where each nonplanar geometry enables a different biomedical investigation. The sinusoidal wave construct allows us to ask if cells embedded in tissues with varying frequencies of undulation experience changes to cell morphology due to the topology of their environment; the transwell-like mogul enables investigation of cell proliferation of cells grown at or within an air-liquid interface; and the multi-region dome facilitates the study of tissue interfaces where a diseased region of cells meets a healthy region of cells, all within a single contiguous tissue. I am currently exploring these questions through multiple cultures where different device versions and/or multiple cell types are engaged to collect biological readouts which demonstrate SNaP as a translatable platform for the investigation of questions in biomechanics and regenerative medicine.

Biodiesel, "an alkyl ester of fatty acid" and type of biofuel, can be used for fueling vehicles and can be produced via transesterification, the process of using the alcohol methanol along with a base catalyst (usually sodium hydroxide) to break down oils and fats that have many triglycerides into fatty acid methyl esters (FAMEs) and glycerol. The viscous triglycerides are broken down into ester bonds and free fatty acids (FFAs), which are not ideal for biodiesel synthesis because FFAs have high melting points, unlike FAMEs. Thus, biodiesel synthesis should be conducted in a manner that reduces the number of FFAs while having a high breakdown of triglycerides into ester bonds. Transesterification that involves alkali/alkyl (like the bases sodium hydroxide (NaOH) and potassium hydroxide (KOH)) as a catalyst can cause soap-FFA reactions, resulting in "emulsification" challenges (Cheng et al 2013) (Hasan et al 2017). KOH and NaOH both can cause soap formation if they interact with triglycerides and esters. Furthermore, KOH produces more soap that NaOH, but KOH also helped produce more biodiesel than that from NaOH at 0.2 mol concentration (Van Gerpen et al 2006). What are the effects of NaOH and KOH on the fuel value of the biodiesel produced over the course of eight weeks? If KOH is used to synthesize biodiesel, then the biodiesel's fuel value form KOH will be higher than that form NaOH. Although the research project is currently in progress, the anticipated result is that KOH better catalyzes transesterification (via causing more heat combustion of ethanol) than NaOH for producing biodiesel. The results' significance determines which catalysts are used to produce more biodiesel. This is because the amount of biodiesel produced can be used for daily life purposes like faster transportation without having to refuel automobiles as frequently.

Proteins in the NFкB family are transcription factors that modulate the expression of genes relating to immunity and inflammation. One protein within this family is the p50/RelA heterodimer which includes a structured DNA-binding domain and a Transcription Activation Domain (TAD) which is intrinsically disordered, or naturally lacking secondary and tertiary structure. Previous studies have shown that interactions between the DNA-binding domain and TAD affect DNA binding affinity and specificity. With the goal of further assessing and comparing the interactions between intrinsically disordered and structured domains in proteins of this family, we have worked to troubleshoot and optimize protocols relating to expressing and purifying human p50/RelA protein. I analyzed the efficiency of multiple chromatography steps and introduced changes to improve yield. Optimization of the expression and purification protocols will enable future investigations into the DNA binding activity of this protein.

Neuronal and endocrine cells store and secrete molecular cargos like neurotransmitters and metabolic hormones through the regulated secretory pathway. Dense-core vesicles (DCVs) originate from the trans-Golgi network and undergo a maturation process involving peptide processing and cargo sorting before being stimulated to release their cargos outside the cell. Dysregulation of this process leads to a wide range of neurological and metabolic disorders; yet the molecular mechanisms underpinning it remain poorly understood. Vesicular traffic are largely coordinated by the Rab family of GTPase proteins.  Previous work identified the conserved proteins TBC8 and RUND1 as regulators of DCV maturation in Caenorhabditis elegans; and both proteins bind active GTP-bound RAB2. TBC8 is the putative RAB2 GTPase activating protein (GAP) which promotes conversion of GTP-RAB2 into GDP-RAB2, thereby inactivating the Rab. RUND1 interacts with both active GTP-RAB2 and TBC8, yet its precise function remains unknown. This study aims to characterize the biochemical function of TBC8 and RUND1 in regulating RAB2 activity. Using purified proteins, we demonstrate that TBC8 greatly promotes RAB2 GTP hydrolysis, indicating it is the bona fide RAB2 GAP. Additionally, we show that RUND1 strongly inhibits TBC8-stimulated RAB2 GTP hydrolysis, suggesting RUND1 may compete with TBC8 for RAB2 binding. Given this interplay between RUND1 and TBC8 in binding RAB2, we hypothesize that RAB2 exhibits exclusively pairwise interactions with its partners. To test this, we will use mass photometry to study whether RUND1 and TBC8 can bind RAB2 simultaneously or if one complex is preferentially formed. Based on our current findings, we propose a model where TBC8 promotes RAB2 inactivation by stimulating GTP hydrolysis and RUND1 blocks RAB2 inactivation by TBC8, prolonging the activate state of RAB2.

Hydrogen sulfide (H₂S), known for its distinct smell of rotten eggs, is recognized as the third endogenous gaseous signaling molecule, alongside nitric oxide and carbon monoxide. Often described as a double-edged sword, H₂S exhibits both cytoprotective and cytotoxic properties depending on the biological context. A 2018 study suggested that H₂S enhances the efficacy of doxorubicin (Dox), an anticancer drug, by promoting apoptosis and reducing colony formation in HepG2 cells, even restoring drug sensitivity in resistant cells. However, my preliminary experiments indicated a protective role of H₂S in HepG2 cells under stress, particularly when treated with NaSH (an H₂S donor). Rather than inducing apoptosis, H₂S appears to support cell proliferation and regulate reactive oxygen species (ROS) production. My research project aims to identify H₂S -dependent pathways in HepG2 cells under oxidative stress. Using Dox as a stress inducer, I conducted viability and cytotoxicity assays, demonstrating that supplementation with 250 µM NaSH at 0 and 12 hours significantly restored cell survival. To investigate the molecular mechanisms, RNA-seq analysis identified 2,996 differentially expressed genes in the H₂S + Dox group compared to Dox alone. Principal component analysis (PCA) revealed distinct transcriptomic profiles, while KEGG enrichment analysis highlighted significant alterations in genes within the PI3K-Akt pathway. To further validate these findings, I plan to perform flow cytometry and western blot analysis. While the role of H₂S continues to be debated, my data suggest a protective function in liver cells against Dox-induced stress via the PI3K-Akt pathway. Understanding these mechanisms could pave the way for new therapeutic strategies aimed at maintaining or increasing H₂S levels to support cell health in diseases characterized by oxidative stress, such as cancer and diabetes.

Pulling apart DNA during replication induces DNA strands to wrap around each other, producing positive supercoils ahead of the replication fork. Positive supercoils hinder further DNA replication, and are removed by Type II Topoisomerases (Top2s), a group of essential enzymes that cleave positive supercoils to relax DNA for easy separation. Errors in supercoil resolution are linked to diseases like cancer and autoimmune disorders. A key question in the field is the mechanism by which Top2s locate positive supercoils. We recently discovered that GapR, an essential DNA binding protein conserved across α-proteobacteria, binds positive supercoils and stimulates the activity of bacterial Top2s DNA Gyrase and Topoisomerase IV. We hypothesized that GapR recruits Top2s to positive supercoils by direct interaction. We investigated this mechanism by using a Bacterial Two-Hybrid assay to screen for GapR interaction with Top2 subunit and identified an interaction between GapR and the A subunits of DNA Gyrase and Topoisomerase IV. Additionally, we discovered that GapR interacts with Top2 A subunits, and not with Top2 B subunits, in a gel shift assay. In collaboration with the David Baker lab, we generated predictions of the GapR-Top2 interaction which together support a model of interaction between GapR and the Top2 A subunit that is mutually exclusive to the Top2 B subunit. In our current work, we aim to identify the mechanism of direct interaction between GapR and Top2s aided by mass photometry and biochemical experiments to reveal a previously unknown mechanism of Top2 recruitment. Because GapR is conserved by alphaproteobacteria, our research could reveal a target for inhibition by antibiotics. If such Top2 recruiters are more broadly conserved, our work provides a novel pathway to target with anticancer therapeutics as human Top2 inhibitors are important chemotherapy drugs.

Cardiac-specific promoters, such as NK2 homeobox 5 (NKX2.5), are essential for driving gene expression during early heart development, making them valuable for studying neonatal congenital heart diseases. However, the large size of the NKX2.5 promoter limits its use in adeno-associated virus (AAV) delivery systems, restricting vector space for therapeutic genes. This study aims to develop a compact hybrid NKX2.5 promoter that retains cardiac specificity while enhancing its efficiency in early-stage cardiac research and gene therapy. To achieve this, we replace the enhancer region of NKX2.5 with a shortened cytomegalovirus (CMV)-derived enhancer, preserving cardiac specificity while reducing promoter size. The hybrid promoter is then cloned into an AAV vector to drive green fluorescent protein (GFP) expression for assessing transcriptional activity and tissue specificity. Following AAV injection into pregnant mice, we will harvest early-stage embryos to evaluate GFP expression in cardiac tissues, comparing the hybrid promoter’s efficiency against the original NKX2.5-driven GFP expression. This study addresses current limitations of cardiac-specific promoters by developing a streamlined version optimized for gene delivery in neonatal models. Our findings strives to enhance gene therapy strategies for congenital heart diseases and provide insights into early cardiac gene regulation.

The small ubiquitin-like modifier protein, SUMO, regulates the activity of many cellular processes through covalent modification of proteins. These modified targets include the protein components of chromatin; histones H2A, H2B, H3, and H4. Chemical modification of histones directly regulates gene expression, necessitating an understanding of the role of each type of modification. The identification and role of histone SUMOylation has been described for H4 in human cells; however, SUMOylation of H2B in human cells has been recently observed but not yet characterized. SUMO is shown to impose a predominantly repressive effect on many cellular processes and proteins that it targets. Therefore, I am working toward identifying the role of H2B SUMOylation to either add to this narrative or describe novel functions of SUMO. To accomplish this, I have purified wild-type histones and SUMO-histone fusions through bacterial expression followed by size-exclusion and affinity chromatography. The purification of several of these proteins has not been described yet; therefore, I designed the purification for these proteins using unique methods, like solubilizing tags, to obtain the product. I reconstituted the purified proteins into octamers, the protein complex that DNA wraps around, and purified the octamers away from other oligomeric forms of the histones via size-exclusion chromatography. I further reconstituted the octamers into mononucleosomes by condensing DNA around them to mimic SUMOylated nucleosomes in chromatin. I hope to then subject the mononucleosomes to in vitro biochemical assays to observe changes in the modifications that regulate other chromatin-associated proteins. A better understanding of the complex dynamics at play during gene expression and repression is needed to identify stronger, safer, and more sustainable therapeutics. Furthermore, SUMO is implicated in a wide array of diseases, such as Alzheimer’s. Therefore, the results of this study will increase our understanding of gene regulation and provide insight towards treating related diseases.

This study utilizes design research to explore how storytelling informs the design, usage, and knowledge production of a digital archive repository housing digitized memory objects. Ranging from ao dai to math booklets, these memory objects are grounded by narratives of Vietnamese diasporic identity and experiences shared by community researchers as part of Sarah Nguyen’s Sharing Stories, Sharing Trust (SSST) workshop series. To understand how story-driven approaches translate and transform digital archive design, I draw upon multiple methodologies such as case study analysis of existing community-based applications of digital archives and thematic analysis of SSST workshop discussions (formatted as observational memos). I also draw from user interviews with community researchers using a semi-structured, narrative-driven protocol. These analyses inform the design of a digital repository prototype that foregrounds story-driven design whilst exploring possibilities for the preservation and sharing of Vietnamese diasporic experiences.

“In Africa, whenever an old man dies, a library burns down.” –Amadou Hampâté Bâ. Malian writer, historian, and ethnologist Amadou Hampâté Bâ’s quote underlines elders as keepers and purveyors of knowledge, culture, and wisdom. As “libraries” worth prioritizing and preserving, Black grandmothers’ stories and cultural inheritances (material possessions, cultural traditions, rituals, language, etc.) have been integral to the matriarchal traditions and culture characterizing people of African descent. Yet, at key periods, African Americans have experienced threats to our collective ability to document, preserve, and pass down our “libraries” because of a lack of financial resources and technological support. Black grandmothers experience multidimensional oppressions and rarely have a chance for self-representation. What are the ways black grandmothers experience erasure in the digital age, and within their communities through displacement? How are we responding? How can researchers mitigate, document, and disrupt their erasure? To conduct this work, we collect oral histories, document cultural inheritances, and create data visualizations to digitize their "libraries." We document, preserve, and amplify Black culture and history by sharing the lived experiences of Black grandmothers. The Black Grandmother Worldmaking Library is a collaborative, community-based model for gathering, archiving, and digitizing distinct aspects of our “libraries” beginning with the stories and cultural inheritances of Black grandmothers experiencing mass displacement in Seattle’s Central District and along the Gullah Geechee Corridor. The project offers a readily accessible digital resource for Black grandmothers to contribute to and control the stories we tell about their lives. The Black Grandmother Worldmaking Library aims to repair what we are taught about Black grandmothers, to reclaim their narratives and culture using firsthand accounts, and to preserve their legacies.

I am currently assisting PhD student Jessica Luo in her research of the Sanmen Wu sound system, a language of the Wu family found in Southeast China. As Jessica writes an article that summarizes the sound structure of Sanmen Wu, I analyze utterances produced by speakers of the language. In my self-guided research, I focus on the sound quality of the consonants and their variations to determine underlying pronunciation. I also connect these variations to historical sound changes from Middle Chinese, its ancestor, into Sanmen Wu. I observe that Sanmen Wu speakers tend to freely alter pronunciations of certain consonants. For example, a speaker may say 部 [pu] or [bu] meaning ‘part,’ the latter only appearing after another spoken word. These two syllables contrast only in voicing, where [p] is voiceless and [b] is voiced. I use Praat, an industry-standard speech-analysis program, to read diagrams that depict the acoustics of these consonants to verify my findings. I am also creating a set of rules that predicts this alternation. One of the conditions is as follows: words with alternating voicing in their consonants change when pronounced within a sentence (‘medially’). Eventually, I will explain these rules, and I predict my explanation is related to the evolution of Sanmen Wu into its current stage. I reason that because the Wu language family stems from Middle Chinese, both of which require contrastive voicing to create distinct words, Sanmen Wu also contains the original underlying variation that exists in Middle Chinese. As such, I attribute this variation to an inherent part of the language rather than random circumstance. Ultimately, I intend to foster a thorough understanding of Sanmen Wu phonology and provide a foundation for further exploration of this topic.

The title of this project references Stuart Hall’s memoir, Familiar Strangers and encapsulates the experience many artists have when portraying family members they have never met but feel like they know through photographs. Drawing from Tina Campt’s definition of the haptic–how viewers touch or are touched by family photos–I look to Black artists’ uses of photos to express their relationship to themes of family, diaspora, memory, and history. How do Black artists use hapticity and embodiment to engage with family photos and produce alternative ways of conceptualizing identity? How do they view family photos as sites of memory activation? Why and when have these artists returned to family photos as source material?  This focus on hapticity reveals how Black visual artists recreate, re-enact, and revise family photos in their work to produce micro-histories that might otherwise be lost. I analyze artist statements, arts and culture literature, and academic articles to identify individual artists’ approaches to family archives. The featured 19 artists span the African diaspora, and I use Safia Elhillo’s home is not a country as a framework to situate the socio-political contexts of their work, which include the legacy of transatlantic slavery, transnational migration, diaspora, colonialism, racial apartheid. Many of the artists have gained significant attention as they portray family history and collective memory in their practice. This work can guide future exhibitions and continue the ongoing conversation on family photography in Black visual art.

Zanele Muholi is a queer, Black, nonbinary South African photographer who produces work depicting the lived emotional experiences of Black queer South Africans, specifically highlighting individuals who have lived through corrective sexual abuse. While corrective abuse against queer and Black people has been documented throughout the art historical canon, many depictions acknowledge only the physical pain, completely omitting the emotional toll this abuse causes. Acknowledgement of the range of emotion of queer and Black individuals in the art world is unfortunately extremely limited, especially when considering depiction of victimized forms; however, Zanele Muholi creates artwork that counters this inadequacy. Through the medium of black and white photography, captured with a “loving” lens, Muholi subverts the concept of corrective sexual abuse by emphasizing the true emotional impact it has through a focus on facial expression and body language, humanizing their subjects to decolonize and reclaim the long-exploited image of the black body from historical degradation under apartheid; they simultaneously challenge accepted gender presentation by depicting queer South Africans who fall outside of the accepted gender binary, making unavoidable the humanity of those who have endured this kind of abuse. Muholi’s work is intended for a wide audience; they want to provide an avenue for queer Black individuals to see themselves in the art world, however; they also want their work to be experienced by those who may be unaware of their communities’ struggles to humanize them to the world. By examining a selection of Muholi’s works alongside historical and contemporary examples of Black pain, and investigating responses to the artist, this paper proves that Muholi’s work questions how Black pain is depicted in media and pushes the boundaries of accepted gender presentation and sexual orientation in the museum space, ultimately creating a fuller picture of the queer Black lived experience.

Maintaining the integrity of genetic material and preventing changes over time is essential for normal cellular function. This genomic stability is directly affected by the DNA replication process. Replication must be both accurate and efficient; mutations that affect DNA replication can cause genomic instability and changes in the genetic makeup of the cell. Through a genomic instability screen in mice, researchers discovered a single base pair mutation in a highly conserved gene required for unwinding DNA during DNA replication. The presence of this single base pair substitution, called Chaos3, in both copies of the gene causes female mice to develop mammary tumors. We have found that in the yeast Saccharomyces cerevisiae, the corresponding Chaos3 mutation decreases activation or “firing” of some replication origins—the sites where DNA replication begins. Chaos3 does not affect all early firing origins in the genome; rather, origins near centromeres are specifically affected, thereby delaying replication of those centromeres, causing chromosome loss. We found that when an affected origin is replaced with an unaffected one, firing levels are restored to wild type function and that chromosome loss is rescued. To further understand what components are essential for timely DNA replication, and why only a subset of origin sequences are sensitive to the Chaos3 allele, I am focusing on the origin sequences directly. I am mutating the origin sequence itself and separately deleting different genes whose products have potential interactions with origin sequences. My research aims to advance the understanding of the role these genes play in the activation of origins for timely DNA replication and how the Chaos3 mutation may be interrupting normal function of these processes. This knowledge can help identify key molecular mechanisms that drive cancer development in higher eukaryotes.

Regulatory T cells (Tregs) play an integral role in self-tolerance and the preventing autoimmunity by suppressing the immune response. As such, inducing Treg expansion is a promising avenue for treating autoimmunity. Previous studies have shown that treatment with an interleukin-2 (IL-2) mutein Fc.Mut24 causes more robust Treg expansion than wildtype IL-2 and is effective at preventing autoimmunity in the non-obese diabetic (NOD) mouse model. In this study, we identified the synergistic roles of the T cell receptor (TCR) and IL-2 receptor in IL-2 Fc.Mut24-mediated Treg expansion, leading to the question of how TCR stimulation is affected during treatment. Classical dendritic cells (cDCs) present antigens to the TCR on Tregs, leading to an increased Treg population to suppress autoimmunity. This study aims to elucidate the role of interactions between Tregs and cDCs during IL-2 Fc.Mut24 treatment using in vivo mouse models. Through the uLIPSTIC (universal labelling immune partnerships by sortagging intracellular contacts) model, we reveal the effect of IL-2 Fc.Mut24 on the frequency of short-range and transient Treg/cDC interactions. Using Zbtb46-DtR bone marrow chimeras to deplete cDCs, we may begin to understand the extent to which cDCs are necessary for the robust Treg expansion typically seen during IL-2 Fc.Mut24 treatment. Preliminary results of cDC depletion do show reduced Treg expansion. We expect to find that IL-2 Fc.Mut24 promotes immunosuppressive Treg/cDC interactions in vivo, as indicated by increased frequency of interaction and cDC-dependent Treg expansion. The findings from this study will contribute to a greater understanding of how IL-2 mutein therapies mechanistically combat autoimmunity, potentially paving the way for identifying new applications to treat disease.

Merkel cell carcinoma (MCC), a rare skin cancer, is mostly driven by integration of the Merkel cell polyomavirus which encodes T-antigen (T-Ag) proteins. Previous research has shown that T & B cells target T-Ag. Indeed, patients with virus-driven MCC produce T-Ag-specific antibodies that are useful to track disease progression. These antibodies do not play a direct role in MCC immunity as T-Ag proteins are intracellular. Our group has recently found that in tumors, T-Ag-specific B cells with germinal center or antibody-secreting phenotypes strongly predict improved MCC outcomes. These intratumoral B cell phenotypes reflect a robust cancer-specific T cell response. In contrast, T-Ag-specific B cells in the blood of MCC patients are predicted to predominantly have a memory or naive phenotype, and it is unknown if they contribute to anti-tumor immunity. We used fluorescently labeled T-Ag-proteins and flow cytometry to assess B cell responses in blood at the time of MCC diagnosis. In total, we analyzed samples from 23 patients whose MCC recurred within 3 years of diagnosis and 24 samples from stage- and age-matched MCC patients whose disease did not recur. We found no difference in the frequency of all circulating B cells (regardless of T-Ag-specificity) between patients who did and did not develop MCC recurrence. In contrast, higher frequencies of total memory B cells (CD27+IgD-IgM-) were associated with an increased risk of disease recurrence (HR 3.67 [1.58- 8.55], p=0.003). Intriguingly, T-Ag-specific memory B cells were also more abundant in the blood of patients who ultimately developed MCC recurrence (HR 2.82 [1.22- 6.53], p=0.012). Together, our results demonstrate that higher frequencies of circulating memory B cells associate with worse MCC outcomes. These findings suggest that the functional state of total and T-Ag-specific circulating B cells reflect their immune response within MCC tumors.

Preterm birth is a leading cause of neonatal morbidity and mortality, with intra-amniotic infection and inflammation being major contributors to early preterm labor (PTL). Despite ongoing research aimed at reducing inflammation in neonates, most studies have focused on post-delivery while few have been done prior to delivery. IL-1 is a central upstream mediator of inflammation in the amniotic cavity and the neonate. IL-1 is a key cytokine that is responsible for induction or propagation of the cytokine cascade responsible for PTL. Rytvela, an interleukin-1 receptor antagonist made up of seven D-amino acids, acts as a selective antagonist of IL-1 signaling, which could be used to act as a therapeutic approach to reduce inflammation and prevent PTL. The purpose of this experiment is to determine if interleukin-1 (IL-1) is a key molecular target for the development of antenatal therapeutics to prevent PTL and fetal injury. We hypothesize that Rytvela administered intravenously to the mother will cross the placenta and be detectable in the amniotic fluid and fetal plasma, suggesting that Rytvela could effectively block IL-1 signaling in the fetus and therefore reduce fetal inflammation. Maternal blood plasma samples were drawn at Day 1, 2, 6 and 10 post infusion. To confirm the transfer of Rytvela to the fetus, we used liquid chromatography-mass spectrometry (LC-MS) to detect the drug, looking at integration, peak identification, and backlog pressures to see if Rytvela is detectable in maternal plasma. Rytvela was detected and luminex plates were run to measure cytokine levels. After GBS infection, Il-1 beta and Il-23 concentrations increased. After Rytvela administration, the concentration of the pro-inflammatory cytokines decreased. Future directions will involve measuring cytokine levels at these time points and correlating them with Rytvela infusion to evaluate the drug’s impact on maternal-fetal inflammation

Bronchoscopy with bronchoalveolar lavage (BAL) is a common approach to assess the graft in lung transplant recipients. However, bronchoscopy is an invasive approach that carries procedural risks. Identifying plasma biomarkers levels which correlate with those measured in BAL fluid enables less invasive investigations. This study aims to determine the correlation between biomarkers measured from plasma and BAL fluid. We analyze paired plasma and BALF (BAL fluid) samples collected from lung transplant recipients undergoing for-cause bronchoscopy (n = 95 individuals and inclusive of 164 encounters). Researchers collect paired samples from each participant within a two-hour timeframe. Researchers measure a panel of 39 biomarkers in samples using electrochemiluminescence assays. We evaluate plasma/BAL correlation data using Pearson correlation coefficients on log-transformed concentrations. Among participants, the average age is 61 years, 74% are male, 93% are white, with Restrictive lung disease (60%) being the most common pre-transplant pulmonary disease. The median time from transplant to bronchoscopy is 412 days (IQR: 194-741). Results indicate that correlational data is highly variable. The two most highly correlated biomarkers are IL-12/IL-23p40 (r = 0.67) and CXCL10 (r = 0.64). There are no biomarkers that have significant inverse correlations. The levels of 11 out of the 39 measured biomarkers show moderate correlation, ranging from r = 0.20 to r = 0.45. Many of these biomarkers are chemokines related to immune cell migration to the lung (e.g., CCL2, CCL3, CCL4, and CCL22). A key implication of this finding is that researchers should exercise caution when extrapolating alveolar biology from circulating (plasma) samples. Future analyses will test whether the ratio between paired BALF and plasma biomarker levels provides biological or clinical insight beyond using these biomarkers measured in isolation.

Given a set of goods and a set of individuals, one might ask what the optimal way to divide the goods among the individuals is. This is known as a bargaining problem. Bargaining theory is a set of mathematical tools which can help us answer these sorts of questions. Assuming that the individuals’ preferences can be represented numerically, a bargaining solution concept tells us the optimal division of goods, called the solution to the bargaining problem, among the individuals. In some cases, solutions to bargaining problems involve randomly choosing how some or all of the goods are distributed. Of interest to us is the fact that the solutions to these bargaining problems may fail to be continuous, in a certain sense. If the strengths of the individuals’ preferences are changed even slightly, it may be the case that the optimal division of goods changes drastically. Broadly speaking, the goal of this project is to understand when and why this phenomenon occurs. I begin by formally defining what it means for the preferences of the individuals, as well as the sets of solutions to the associated bargaining problems, to be close to one another. I then prove that under certain conditions, small changes in individuals’ preferences cannot result in large changes in bargaining solutions. I am currently still working on proving that if these conditions fail to hold, then one can slightly modify the individuals’ preferences in such a way that the associated bargaining solutions change quite substantially. We hope that these results can be applied to justify randomization amongst options in collective decision making problems, particularly those related to experimental design.

Since the ban on sports betting was struck down by the supreme court in 2018, 38 states have legalized betting in some form. In the third quarter of 2023, sports betting generated over $500 million in tax revenue for state governments. Many of the impacts that seem obvious when thinking about the consequences of legalizing sports betting have already been studied, so in this paper I analyze effects that are further downstream in the causation chain. Specifically, I look at how the legalization of sports betting has affected marital relationships as measured by state-level divorce rates, mental health outcomes as measured by depression rates, and substance abuse issue measured by the number of alcohol related hospitalizations and rehabilitation center bookings. I utilize the staggered rollout of legalization across the country to conduct a difference-in-differences analysis to accurately measure the magnitude of each of these effects. Additionally, I investigate the potential additional damages caused by the legalization of online gambling compared to only in-person gambling. Of the 12 states who have yet to legalize any form of sports gambling, most of them have some form of legislation on the table to decide the future of sports betting in their respective states. Within these legislative sessions, and eventually if these measures are on state ballots,legislators and voters will be asked to personally weigh the pros and cons that are associated with the legalization of sports betting and this paper's aim is to be a small part in helping inform these decisions.

What explains variations in how ports are acknowledging and responding to the challenges of climate mitigation and climate adaptation?  This research project examines the response of the top 100 global ports (in terms of tonnage) across the world to the growing challenges posed by climate change. Ports face challenges such as reducing emissions from ships and port operations, and adapting to changes like sea level rise, irregular water flows (crucial for ports on river estuaries), shifts in cargo composition, and changing water dynamics. I will explore whether these ports are acknowledging climate challenges and the extent to which they are establishing clear targets and addressing them in their operational strategies with clear timelines. Moreover, how they are preparing for the eventual decline in global fossil fuel trade. In particular, I will pay special attention to coal-exporting and importing ports, analyzing if they continue to make investments in coal infrastructure and whether they have initiated plans for diversifying their revenue streams to prepare for the eventual phase-out of coal. I have already started collecting data by closely examining the websites of these ports. I will create a database of whether these ports have developed climate statements that identify environmental issues, set clear targets with timelines, and outline strategies to mitigate and adapt to these challenges.  I will combine the scores on these dimensions to create a climate score for each port. In addition to my quantitative analysis based on a dataset created by website research, I will conduct interviews with port officials and union leaders at the Port of Seattle, Tacoma, Everette, and Bellingham.

Periodontitis is a severe inflammatory disease that damages the gingiva and has been linked to systemic diseases, such as diabetes, heart disease, and respiratory disease. These serious health complications express the importance of studying oral microbiota and their interactions. This research investigates the growth dynamics of Fusobacterium nucleatum and Porphyromonas gingivalis, two gram-negative anaerobic bacteria that play a significant role in inducing the progression of periodontitis, under mono- and co-culture conditions. By collecting monoculture and co-culture growth curves along with cell counts, and LIVE/DEAD BacLight staining we are identifying their optimal growth phases and interactions. With this information, we seek to optimize these cultures for downstream experiments, including bulk and single-cell RNA sequencing, to identify unique genes signatures from cell-cell interactions implicated in periodontal disease progression. Understanding these dynamics will contribute to future studies on the persistence of periodontal infections and broader research on gene expression.

Older adults recovering after hospitalization in an intensive care unit (ICU) are at high risk of functional decline. Older adult ICU survivors often report symptoms of cognitive impairment, sleep disturbances, and pain, which can complicate functional recovery. In addition, certain social determinants of health (SDoH) are associated with worse cognitive and physical outcomes that lead to functional decline in older adult ICU survivors. Little is known about the relationships between patient-reported symptoms (e.g., cognitive function, sleep quality, and pain intensity), selected SDoH, and functional recovery for older ICU survivors during hospitalization. This project has two overall aims: 1) explore associations between patient-reported symptoms of cognitive function, sleep quality, pain, and SDoH; and 2) explore associations between these variables and successful participation in physical therapy and/or occupational therapy (PT/OT). We collected and utilized data from two ongoing randomized controlled trials. Older ICU survivors hospitalized at University of Washington Medical Center or Harborview Medical Center were recruited and enrolled. Participants answered the PROMIS Cognitive Function Abilities, Sleep Disturbances, Sleep Related Impairment, and Pain Intensity questionnaires to evaluate self-reported cognitive function, sleep quality, and pain intensity. We did chart review of electronic health records to gather relevant information regarding SDoH, and length of PT/OT participation in minutes. We examined the differences using t-tests, Chi-squared tests, and ANOVA for binary, categorical, and/or continuous variables, respectively. We used descriptive analysis to explore trends between self-reported pain, sleep quality, and selected SDoH on self-reported cognitive function and participation in PT/OT. Results from this project will inform the design of subsequent clinical trials, which could aid in the development of personalized interventions aimed at reducing functional decline in older ICU survivors. 

Xylazine is a veterinary sedative that has become a common adulterant in fentanyl products due to its ability to prolong the euphoric effects of fentanyl. Adulterated drug mixtures containing xylazine have been linked to an increased risk for respiratory depression and fatal overdose. Existing treatments for overdose such as naloxone do not work against xylazine and there is currently no FDA approved reversal agent for xylazine toxicity. Monoclonal antibodies (mAbs) are a promising therapeutic option to reverse drug overdose and can be used to target small molecules by sequestering them in the bloodstream and preventing their passage into the brain. Previously, we made a series of xylazine haptens and formulated them into vaccines where they were found to induce strong antibody responses, reduce brain to serum ratio of xylazine, and mitigate respiratory depression in Sprague-Dawley rats. Based on the protective effects of our xylazine conjugate vaccines, we hypothesized that we can create an effective reversal agent by isolating xylazine specific mAbs. In this study, we immunized mice with xylazine conjugate vaccines to generate antibodies specific against xylazine. We then used the secondary lymphoid organs of the vaccinated mice to establish stable mAb producing cell lines using hybridoma technology. Hybridomas were screened with ELISA and lead candidates were selected and sequenced for further characterization. We will conduct in-vitro characterization assays to quantify binding affinity, functional activity, and thermostability of our lead mAbs. Furthermore, in-vivo studies will assess the efficacy of our mAb lead candidates in rodent models.

TBC domain containing kinase (TBCK) is an understudied protein with three domains: a pseudokinase; Tre-2, Bub2, and Cdc16; and rhodanese, and is highly expressed in the brain. Homozygous mutations in TBCK cause a rare neurodegenerative disorder in children, which clinically presents as syndrome infantile encephalopathy, brain atrophy, cerebellar hypoplasia, and muscle hypotonia. Two mutations in particular, Arg126Stop and Arg511His in the pseudokinase and TBC domains respectively, are commonly found among TBCK patients. The progression of the disease is characterized by a global regression in brain development, severe intellectual disability, and premature death in acute cases. The pathogenic mechanism underlying TBCK syndrome is unclear, but past studies show that TBCK patient neurons demonstrate aberrant metabolite buildup in the lysosome likely resulting from abnormal lysosomal activity. Immunoprecipitation mass spectrometry was performed for wild type TBCK in both N terminal and C terminal tags, revealing a preliminary list of both known and unknown interactors for TBCK. To further investigate the early developmental implications of mutant TBCK, CRISPR/Cas9 directed mutagenesis is being used to generate two induced pluripotent stem cell (iPSC) lines harboring the Arg126Stop and Arg511His mutants for subsequent differentiation into neural progenitor cells (NPC) and neurons. Immunofluorescent imaging of the mutant NPCs will confirm the recapitulation of growth and lysosomal defects present in patient cells. To analyze the effect of TBCK mutation on lysosomal function/content, we will immuno-isolate lysosomes through lysosome immunoprecipitation (Lyso-IP) and identify proteomic changes through mass spectrometry. While providing a crucial in vitro cell model of two common patient mutations, these experiments will offer critical insight into cellular dysfunctions that contribute to TBCK disease states.

Historical archaeologists understand toys in the material record to explicitly mark past activities of children. This project focuses on the play activities of enslaved children on North American plantations through the toys they left behind. We used data from the Digital Archaeological Archive of Comparative Slavery (DAACS) to explore the material evidence for identity formation and socialization of enslaved children based on existing studies on enslaved childhoods. Specifically, we investigated the following questions: what materials and manufacturing techniques were most frequently used in the creation of the toys of enslaved children on North American plantations? Based on the associated costs of these materials, what is the range of expense exhibited by enslaved children's toys? What role might toys have played in enslaved children’s agency or passivity in socialization? To address these questions, we queried the DAACS repository concerning object specifications like material and manufacturing technology for toys excavated from North American plantations. This data was imported into RStudio, where we used programming packages to clean it and create visualizations to convey trends. Our pilot project (48 toys) found that porcelain and a molding technique were most frequently used, materials with varying expenses were present, and some toys exhibited post-manufacture modifications. We now have data on 599 toys from 41 sites on 13 plantations, greatly improving our representation of enslaved children in the material record. In this poster we present the result of our analysis of this large data set and compare the locations. The findings of this research will help to fill in gaps of a larger conversation about the relationship between childhood play and race, and more broadly contribute to archaeology’s attention to past social dynamics.

Copepods are an essential link between micro- and macroscopic trophic levels in Salish Sea food webs. The distribution of copepods across spatial and temporal scales is well-known and is partially attributed to physical oceanic processes. However, few studies have characterized copepod densities at different tidal heights in the San Juan Channel. This study investigates copepod densities at depths of 0-25m and 0-50m during high and low slack tides when tidal currents are at their lowest velocity. Higher overall copepod densities were expected during slack high tide due to the influx of oceanic water from the Strait of Juan de Fuca. Samples were collected over four days in the northern San Juan Channel during September 2024. Twelve vertical plankton tows were performed with six replicates for high and low tides respectively. Samples were diluted and randomized using a plankton splitter, creating 5ml aliquots to calculate copepod density. Copepod densities from 0-50m depth during slack high tide were significantly higher (p-value < 0.001) than all other samples. No difference in copepod density was found between 0-25m and 0-50m depths during slack low tide. Increased tidal height resulted in higher copepod densities for low and high slack tides. Our findings suggest the physical processes within the San Juan Channel, such as the influx of colder, saltier waters during slack high tides increase copepod densities in the top 50m of the water column. These shifts in copepod densities may impact the feeding behavior of higher trophic levels in the San Juan Channel food webs.

The first-in-class capsid (CA) binding antiretroviral, Lenacapavir (Len), inhibits viral spread at multiple steps in the viral life cycle. Structural studies show that Len interacts with an FG-binding pocket between the N-terminal and C-terminal domains of adjacent CA monomers resulting in destabilization of the CA core lattice. Three key binding functional groups within Len that interact with CA were identified. Subsequently, six Len analogues (Lenalogs) were designed and synthesized. These Lenalogs vary by the removal or replacement of one of the identified functional groups. My work investigates the impact of Len and Lenalog binding on CA assembly rate, as well as, the structure of the assembled protein. Using an IPTG  E. coli expression system and ion exchange chromatography, I have expressed and purified CA protein. I induced in vitro assembly of the purified CA protein by the addition of inositol hexakisphosphate (IP6) in both the presence and absence of Len or the Lenalogs. Relative to Len, LL-10.4 and LL-15 promoted assembly, LL-14 was similar, while LL-11, LL-19 and LL-20 promoted assembly to a lesser extent. Samples with LL-10.4 and LL-15 were chosen for cryo-EM analysis as these promoted assembly to a greatest extent. CA was assembled on lipid vesicles (templated CA-like particles or CLPs) by the Dick lab (Emory University, Atlanta, GA), and these were subjected to cryo-EM data collection and analysis. Both LL-10.4 and LL-15 bound to the FG-binding pocket like Len. Negative stain transmission electron microscopy and light scattering will be used to further assess the effect of Len and Lenalogs on assembly kinetics. My work will be used to inform the design of next generation CA-targeting antiretrovirals.

This study aims to understand users’ needs in designing a mobile application that assists Cardiopulmonary Resuscitation (CPR). This study is designed through a two-stage online interview, beginning with a screening survey that asks about participants’ occupations and experience with CPR, followed by the main interview that asks about their challenges when performing CPR and their opinions on the most efficient type of feedback. Eight participants who completed the survey included CPR instructors, paramedics, firefighters, and medical students with experience ranging from 3 to 20 years. The participants rated maintaining compression depth as more challenging (7.63 out of 10) compared to maintaining compression rate (5.25 out of 10) when performing CPR, with 10 representing the highest level of difficulty. Participants also reported that visual feedback would be more beneficial for compression depth and auditory feedback for compression rate. Therefore, these findings suggest that an effective assistive CPR device should have real-time visual feedback to aid in-depth consistency while auditory cues support rhythm accuracy similar to a metronome. By leveraging these findings, the proposed application has the potential to enhance CPR effectiveness, improve user confidence, and ultimately increase patient survival rates.

Neonatal hypoxic-ischemic encephalopathy (HIE) occurs when the brain receives insufficient oxygen and blood supply before or during childbirth. HIE is a leading cause of neonatal mortality and morbidity that may also affect later brain development, specifically gyrification - folding of the cerebral cortex creating gyri and sulci. The nonhuman primate (NHP) brain is gyrified, similar to humans, making NHPs a highly translatable model to examine brain development after injury, which has not been well-studied in HIE. In our nonhuman primate (NHP) model of neonatal HIE, we induced injury through in utero umbilical cord occlusion (UCO) for 20 minutes, mimicking the cause of HIE in humans. Twenty-two term-equivalent pigtailed macaques (Macaca nemestrina) underwent UCO and were randomized to no treatment (n = 11) or treatment with therapeutic hypothermia and erythropoietin (TH + Epo [5x1000 U/kg]; n = 11), while non-UCO animals served as controls (n = 7). All animals were delivered via cesarian section. Injury severity was determined by physiological parameters (Apgar score), lactate, and pH levels after resuscitation. To evaluate the impact of injury on gyrification, we will utilize magnetic resonance imaging (MRI) taken 6-months post-injury to measure the gyrification index (GI). GI will be calculated by taking brain’s inner-to-outer hemispheric ratio; the inner trace following the contours of the gyri and sulci, and the outer trace following the circumference of the cerebral cortex. We hypothesize that global and regional GI will be altered in animals exposed to UCO, corresponding with decreased brain volume and greater injury. We also hypothesize that treatment will mitigate some of these changes, leading to a GI closer to control. These results will help determine whether hypoxia-ischemia alters the trajectory of cortical development, as well as the association between injury severity, brain volume, and gyrification.

Pregnant women infected with influenza A virus (IAV) are at higher risk of morbidity, mortality, and poor fetal outcomes. However, the difference in the pathogenesis of IAV between pregnant women and non-pregnant women remains inadequately understood, primarily due to the lack of animal studies that use a translational model of infection. I hypothesized that higher IAV viral load and Type I interferon concentrations would be observed in the lungs and bronchoalveolar lavage of pregnant pig-tail macaques compared to non-pregnant macaques, and that correlating these metrics would yield different results across groups. We inoculated pregnant (n=11) and non-pregnant female (n=18) pig-tail macaques (Macaca nemestrina) with IAV H1N1 (A/California/07/2009) and euthanized them at 5 days post-inoculation, when we expected to observe peak lung pathology. We tested pulmonary function at baseline and study endpoint and conducted clinical assessments daily. I extracted RNA and performed quantitative polymerase chain reactions on the samples to calculate viral load. I also performed enzyme-linked immunosorbent assays to quantify concentrations of Type I interferons (IFN-α, IFN-β). Lastly, I analyzed pulmonary physiology data and clinical assessment scores as a reliable measure of disease severity. A bi-modal distribution of viral load was observed in the lungs of pregnant animals (high>9e5 copies/mg; low<2e4 copies/mg), which was not observed in non-pregnant animals.  When correlating viral load at 5 days post-inoculation with Type I IFN in the lung of the pregnant animals, I found a significant positive correlation between IFN-β and viral load in both the lungs (ρ=0.8, p=0.03) and BAL (ρ=0.9, p=0.02). These results suggest that despite a strong IFN-β response in the lung, a high viral load persisted in the pregnant animals. Next steps could explore whether the kinetics of the pulmonary innate immune response is delayed in pregnancy, which impairs viral clearance. 

Geographic Information Systems (GIS) are a powerful framework that enables the analysis of spatial data, or information connected to a location, that can be applied to a variety of fields, such as public health, policy, agriculture, and environmental management. With these frameworks, we can create maps to convey specific data or general information, make comparisons between data sets, and quantify spatial characteristics. In this study, I utilized a GIS framework together with Real-Time Kinematic Global Navigation Satellite Systems (GNSS RTK) methods to collect spatial data regarding hiking trails throughout Saint Edward State Park in Kenmore, Washington. I hypothesize that the positional accuracy of data collected via GNSS RTK is significantly better than positions collected via methods that do not incorporate differential correction. To test this hypothesis, I will collect differentially corrected positional data along trails in the park and compare them to uncorrected data gathered between 2013 and 2015 from the same trails. Comparisons will be made using a t-test to determine whether there is a statistically significant difference between the mean differences of each data set. Furthermore, I will use this spatial data to visualize more accurate trail locations, indicate areas requiring maintenance, and decommission unofficial trails that are harmful to the ecology in the park.

The Miocene Climatic Optimum (MCO) (17-14 Ma) represents the most recent significant global warming event and provides valuable insights into the future of our planet with higher CO2 levels and warmer temperatures. The Mascall Formation in central Oregon contains a fossil plant assemblage that reflects the vegetation present during the height of the MCO. Despite over 50 years of research in this formation, there is still much to learn about the ancient plant community. For instance, a fossil specimen, consisting of several leaves, that was collected recently exhibits similar trait to bamboo, which represents a new fossil finding in this formation. This project seeks to confidently assign this specimen to the bamboo subfamily Bambusoideae. By analyzing morphological and vein architectural features of the leaves using various microscopic techniques and digital photography. In addition to studying the specimen itself we explore the fossil plant silica bodies (phytoliths) also present in the surrounding substrate to provide independent evidence that bamboo was present in the region. The phytoliths can then be compared to those of current Native American bamboo to find evidence for relatedness or if it was part of some other lineage of bamboo, whether extinct or still present in South America or Eastern Asia. If the specimen turns out to be bamboo, it would have implications for the climate and ecology of eastern Oregon during the MCO as bamboo was not assumed to have previously been present.  

Cave formations, also called speleothems, are natural archives of past climate conditions. Analysis of these speleothems can provide information about environmental changes over thousands of years. Church Mountain Cave is in the Northeast Cascades and is distinctly characterized by its unusually predominant speleothems, which is relatively unusual for western Washington. This project explores the potential of Church Mountain and other caves as paleoclimate archives. I begin with a characterization of Church Mountain Cave, focusing on cave morphology, stratigraphic and structural position of the cave, and forming a hypothesis of cave formation and fault activity. This classification will allow for a detailed view on Church Mountain Cave and the factors impacting speleothem formation. We also characterize a range of speleothems from other caves using trace element and isotope analysis, with the eventual goal of using uranium-thorium dating to establish precise ages and stable isotope analysis with oxygen isotopes to infer past temperature, precipitation patterns, and other environmental factors. By refining regional paleoclimate reconstructions, we can improve predictions of future climate trends and extreme weather events. Additionally, this study underscores the importance of caves as climate archives and highlights the need for conservation efforts to protect these valuable and fragile environments for continued scientific research. 

This research project aims to investigate the perceptions of physical disability among able-bodied college students, with a focus on how the duration of the disability influences these perceptions. Despite increasing awareness and advocacy for disability rights, stigmatization and misconceptions persist within educational environments, potentially affecting the social integration and academic experiences of disabled students. Furthermore, individuals with permanently disabling physical impairments may experience different treatment than individuals who are temporarily disabled by acute injuries. Though anthropological mixed methods research on the perception of disabilities is not uncommon, my research is focused on the difference in the perception of congenital (e.g. cerebral palsy) or acquired permanent physical disabilities (e.g. traumatic limb loss) compared to that of temporary disabling acute injuries (e.g. traumatic fracture). I hypothesize that there is a difference in the treatment of people with permanent versus temporary disabilities; students with permanent disabilities are regarded as “more disabled” than those with temporary disabilities and are considered “less capable” and “less threatening”, and therefore more likely to receive pity and unsolicited help from abled students. They may also be perceived as “less intelligent” despite having no mental impairment. This study's findings fill the gap in the existing body of knowledge on the effect that the duration of physical disability has on its perception. My research employs a mixed-methods approach, combining anonymous surveys and qualitative interviews to explore the attitudes and beliefs of students at UW regarding their peers with physical disabilities. By understanding how the duration of disability affects perceptions, universities can better address the specific needs and challenges faced by disabled students, promoting a more equitable and empathetic academic community.

Cancer immunotherapy, specifically Adoptive Cell Therapy (ACT), has revolutionized treatment approaches using genetically modified T cells to recognize and eliminate cancer cells. However, tumors combat this by creating an immunosuppressive tumor microenvironment (TME) blocking effective antitumor immune responses.  Dendritic cells (DCs) are innate immune cells that act as messengers between the innate and adaptive systems.   In the Oda lab we have designed Dual Costimulatory Receptor (DCRs) that combine a FLT3L or CD40L ectodomain with different costimulatory endodomains (e.g. CD40, 4-1BB, OX40), to provide both T cell-extrinsic and -intrinsic costimulatory signals.  These DCRs are expressed on the surface of antigen specific T cells, and the combination of these signals allows for enhanced tumor antigen presentation and dendritic cell activation, leading to an increase of the immune response to target and destroy cancer tumors. I will investigate how incorporating DCRs on T cells will enhance ACT effectiveness. I hypothesize these DCR signals on T cells will enhance dendritic cell function in the TME, allowing for increased T cell activation and antitumor immune responses. To test this, I will conduct in vitro coculture experiments to determine how DCR-T cells, dendritic cells, and pancreatic cancer cells interact together. I will study the interactions of these immune cells using live cell imaging technology such as the Incucyte. Additionally, I will analyze the phenotypes of our distinct cell populations via flow cytometry.  This research aims to enhance the development of immunotherapy for Pancreatic and all solid cancers by improving the recognition of cancer cells from the immune system. These results could help pave the way for improving solid tumor cancer treatment.

The effectiveness of a drug candidate depends on its ability to distribute to its target site of action after administration. Thus, a primary concern for drug delivery labs like the Pun lab is preventing drugs from being cleared from the bloodstream by the body's renal system before they are able to accumulate to therapeutic levels at their site of action. In short, one important goal in drug delivery research is to find ways to extend a drug's blood circulation half-life. Conjugating drugs to the large molecular weight molecule polyethylene glycol (PEG) to slow their clearance kinetics is the current gold-standard method, but a crucial drawback is that PEG's large size leads to its potentially toxic buildup in tissues like the liver. To get around this problem, my project aims to develop a drug delivery platform that will allow small molecule drugs to reversibly bind, or in other words "hitchhike" onto human serum albumin (HSA), an abundant protein in blood plasma with an extraordinarily long half-life. At this point in my project, I have successfully synthesized a novel fatty acid monomer with a methacrylate functionality that can be used to copolymerize the monomer with therapeutic small-molecules or peptides to improve their circulation half-life. The next steps will be to copolymerize the fatty acid monomer with pGmMA, a water-soluble polymer, and use biolayer interferometry to test the fatty acid monomer's ability to coordinate to albumin, which will confirm its efficacy as a drug delivery platform. If successful, this project has the potential to provide a generalizable improvement to the pharmacokinetics of various kinds of small-molecule drugs or peptides, enhancing their potency and overall ease of treatment. 

Serotonin serves a vital role in the regulation of stress responses, and variance in the release of serotonin was found to contribute to various mental illnesses such as anxiety and depression. Current mental health treatments heavily rely on Selective Serotonin Reuptake Inhibitors (SSRIs). While these medications are generally effective, there are patient populations for whom SSRIs show limited efficacy. Recent studies found that in response to stress, the expression of the FKBP5 gene also increases and modulates many neuronal pathways including serotonin. This experiment determined whether manipulating FKBP5 gene expression in the dorsal raphe (DRN) directly correlates with serotonin release in the basolateral amygdala (BLA), an established neural circuit for fear. To manipulate FKBP5 gene expression, an adeno-associated FKBP5-Cre virus was injected into the DRN of Pet1-Cre transgenic mice, causing up or downregulation of FKBP5 in the DRN. To gauge the effects of FKBP5, fiber photometry was used to measure the release of serotonin following optogenetic activation of the DRN-BLA pathway using a 5HT GRAB sensor injected into the BLA. We hypothesize that increased FKBP5 expression in the DRN will increase serotonin release to the BLA, and as FKBP5 expression is decreased, the release of serotonin to the BLA will decrease. Success in modulating serotonin release using FKBP5 gene expression will expand therapeutic targets in mental illness research, mitigating the gap in treatment efficacy for patients who have undergone ineffective SSRI therapy.

Dynamics of activity across the cerebral cortex at the mesoscopic scale – coordinated fluctuations of local populations of neurons — are essential to perception and cognition and relevant to computations like sensorimotor integration and goal-directed task engagement. However, understanding direct causal links between population dynamics and behavior requires the ability to manipulate mesoscale activity and observe the effect of manipulation across multiple brain regions simultaneously. Here, we develop a novel system enabling simultaneous recording and manipulation of activity across the dorsal cortex of awake mice, compatible with large-scale electrophysiology from any region across the brain. Transgenic mice expressing the GCaMP calcium sensor are injected systemically with an adeno-associated virus driving expression of the ChrimsonR excitatory opsin. This strategy drives expression of the blue-excited calcium indicator, GCaMP, in excitatory neurons and red-excited Chrimson opsin in inhibitory neurons. The light channels of the imaging and the opsin do not interfere. We demonstrate widefield single-photon calcium imaging and simultaneous galvo-targeted laser stimulation over the entire dorsal cortical surface and find that the spatial and temporal resolution of the stimulus is suitable for targeting many specific cortical regions in short periods of time. The calcium indicator responded to the laser within 30 ms, and the activity returned to baseline within 100 ms after laser offset. The area of effect was as small as 3 mm² for the lowest laser power or as large as 10 mm² for the largest laser power. Moreover, the preparation is stable over many months and is thus well-suited for long-term behavioral experiments. The ability to stimulate and measure anywhere on the dorsal cortical surface of the brain will allow us to design computational models describing how causal manipulation impacts neural dynamics, especially in the context of designing closed-loop systems to control neural activity and behavior. 

Kaposi’s sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus known to cause Kaposi sarcoma (KS), a cancer of the soft tissues, and several other diseases. KSHV has two distinct replication cycles: a latent and lytic cycle. During latent infection, only a small section of the viral genome, the KSHV latency-associated region (KLAR), is expressed. Spindle cells, the main proliferating cell type in KS tumors, are thought to be of endothelial origin and are primarily latently infected. Due to lowered viral gene expression during latency, these cells have few viral factors to target therapeutically. Cellular factors required for infected cell survival, like altered metabolic pathways, are potential therapeutic targets for latently infected cells. One metabolic pathway altered by latent infection is fatty acid synthesis (FAS). My research focuses on understanding how KSHV infection induces FAS in cells. Since previous research has shown that expression of KLAR is sufficient to increase lipid droplet formation, a measure of FAS induction, I hypothesize that expression of one of the four genes present in KLAR is likely what upregulates this metabolic pathway. To test this hypothesis, I infected telomerase-immortalized microvascular endothelial (TIME) cells with lentivirus containing a viral plasmid overexpressing one of the four KLAR genes. I then measured lipid droplet formation across each transduced cell population using a flow cytometer. This project is still in progress; however, if the increase in lipid droplet production in transduced cells is similar to the increase observed in cells latently infected with wild-type KSHV, then I will conclude that the over-expressed gene was sufficient to up-regulate FAS. Identifying which viral gene induces FAS in infected cells will provide a new direction for future mechanistic studies and aid in identifying potential therapeutic targets for KSHV-associated diseases.

Visual word interpretation involves both phonology, sound-based processing common in alphabetic languages, and orthography, visual pattern recognition common in logographic languages. Previous research suggests that word recognition in alphabetic languages, such as English, activates the left inferior frontal gyrus (LIFG), and logographic languages, such as Mandarin, engage the visual word form area (VWFA). The goal of this study is to investigate the neural and behavioral differences between native English speakers and native speakers of logographic languages when processing English phonemes. I hypothesized that native English speakers would show more activation in the LIFG whereas native logographic language speakers would show more activation in the VWFA. Participants completed a rhyming judgment task based on English phonemes while undergoing functional magnetic resonance imaging (fMRI) to measure neural activation. English proficiency was recorded through both self-report and the Nelson-Denny Comprehension test. Behavioral results suggested that native logographic language speakers had significantly longer response times and lower accuracy compared to native English speakers. Both self-reported and objectively measured English proficiency were negatively correlated with response times and positively correlated with accuracy. Although the neural analysis did not yield statistically significant results, there was a trend of increased VWFA activation in native speakers of logographic languages compared to English.

This research aims to enhance the food literacy of volunteers at the University of Washington (UW) Food Pantry by providing foundational knowledge on food security, food policy, nutrition, dietary needs, and allergies. Many pantry volunteers lack a background in nutrition or public health, which limits their understanding of the complex issues surrounding food insecurity and food literacy. Through the Winter 2025 Food Systems, Nutrition, and Health Capstone project, my team and I will create a comprehensive brochure that will be incorporated into the pantry’s volunteer training materials. The brochure will include sections on the pantry’s background and goals, the scope of food insecurity among college students both at UW and across the nation, food policies that affect access to nutritious foods, and basic nutrition education. Our objective is to foster empathy and understanding among volunteers, encouraging a deeper connection to the shoppers they serve and the challenges faced by people who rely on the pantry. At the end of the quarter, my team will present the brochure along with other deliverables to community stakeholders. In Spring quarter, I will administer a pre-survey to pantry volunteers to assess their current food literacy and knowledge of food insecurity. Following the brochure’s distribution and review, volunteers will complete the same survey, allowing for an analysis of any changes in their understanding. The study will evaluate whether the brochure improves volunteers' knowledge of food insecurity, ultimately testing if this intervention leads to better food literacy outcomes. If the brochure proves effective in this regard we also hope it will foster increased empathy among pantry shoppers and volunteers.

Language input is necessary for language development. Importantly, mothers have been shown to speak to infants more than fathers do. My study asks whether this pattern extends to the amount of music that mothers produce or play to infants. Music impacts people neurologically, emotionally, and even physically, and can possibly be used to enhance the linguistic development of infants alongside speech. I am comparing the amount and type of speech and music heard by infants in mother-father families to infants in mother-mother families to isolate the variable of gender and gauge its association with infants’ auditory input. Daylong Language ENvironment Analysis (LENA) recorders are used to record everything in an infant’s naturalistic environment (at home) therefore capturing how many instances of in-person and/or electronic speech or music occur and whether parents’ speaking and/or singing is directed to the infants. Undergraduate students are currently annotating LENA recordings of twenty-one mother-mother families (ages 3-24 months) and twenty-three mother-father families (ages 6-24 months) for the amount and type of speech and music present in infants’ audio environments. Annotators indicate what is heard in 100 randomly sampled 10-second segments from each daylong recording. Using independent samples t-tests, I am analyzing the differences in the average amount of music, the average amount of speech, and the type of music presented to infants of mother-mother families versus infants of mother-father families. I hypothesize that there is significantly more speech and music heard by infants in mother-mother families compared to infants in mother-father families. I also hypothesize there is significantly more singing heard by infants of mother-mother dyads, but a comparable amount of electronic music. If found, these results will point to gender being associated with auditory input variability, expanding the knowledge on environmental factors that influence infant language development.

Approximately 18% of older adult intensive care unit (ICU) survivors with delirium are diagnosed with Alzheimer’s disease or related dementia (ADRD) within three years of hospitalization. The constant, 24-hour ICU care can cause disruptions to sleep quality and the biological circadian rhythm. These disturbances, which affect up to 80% of ICU patients, can decrease the efficacy and benefits of interventions to manage delirium and improve cognitive function. We aim to explore the roles of individual chronotypes (morning, afternoon, or evening preference) and self-reported cognitive function on acceptability and adherence to a computerized cognitive training (CCT) intervention for older adult ICU survivors.  Data from two ongoing randomized controlled trials (the SLEEP-COG Study and OPTIMIZE Study) are utilized for this project. Older adult ICU survivors hospitalized at University of Washington Medical Center or Harborview Medical Center are enrolled based on the following eligibility criteria: ages 60 and older, functionally independent prior to hospitalization, and within 48 hours after transfer from intensive care to acute care. Participants who are randomized to CCT complete 30-minute daily sessions for up to 7 days or until discharge. Participants answer the Composite Scale of Morningness questionnaire to determine their individual chronotype and complete the PROMIS Cognitive Function & Cognitive Function Abilities instruments to examine self-reported cognitive function. Upon completion of the CCT intervention, participants answer Likert-type surveys and open-ended questions about feasibility, acceptability, and usability.  Analyses will explore trends between chronotype, self-reported cognitive function, and acceptability.  Differences will be described using t-tests, Chi-squared tests, and ANOVA for binary, categorical, and/or continuous variables, respectively. Potential future directions may include the development of personalized interventions that integrate individual chronotype and perceived cognitive ability to minimize delirium and cognitive decline associated with ADRD in older adult ICU survivors. 

Westfield Southcenter Mall, located in Tukwila, Washington, is one of the largest malls in the nation, and like many malls, its aging retail spaces and surrounding strip malls are becoming less viable. With rising housing costs and a growing regional population, it is clear that spaces like Southcenter must be transformed into affordable, mixed-use districts that can provide housing, vibrant community spaces, and accessible transportation options. This project explores how Southcenter Mall can be redesigned using New Urbanist principles to foster a thriving community. Using site visits and global case studies of recent successful mall redevelopments, it analyzes the current shortcomings of Southcenter Mall and proposes a more successful mixed-use alternative. The final deliverables include a 3D model mock-up of a revitalized Southcenter that includes affordable housing, ground-level retail, and an overhauled transportation framework prioritizing pedestrians and cyclists.

Previous research has determined that nanoparticle systems require a wide parameter space to effectively conduct synthesis and characterization. As a result, the development of high-throughput techniques is essential for efficiently analyzing the large datasets produced in colloidal particle experiments. These methods enable the rapid assessment of particle properties, such as size, shape, and charge, which are critical for modifying nanoparticles for specific applications. In order to do this, advancements in automated synthesis platforms, such as the Jubilee automated multi-tool system, offer the potential to streamline the fabrication of magic sized clusters. This approach has the potential to accelerate the discovery of novel nanoparticles but also allows for real-time adjustment of synthesis parameters to achieve desired properties with high precision, throughput, and reproducibility. As a result of the optimized synthesis process, characterization using techniques such as small angle X-ray scattering (SAXS) and UV-vis spectroscopy can be done at an accelerated rate. Efforts to enhance the durability and performance of the Jubilee automated multi-tool platform are focused on integrating advanced materials to improve system lifespan. This work will incorporate glass syringes and resin-printed components which offer improved chemical resistance and precision compared to traditional plastic components, extending the utility of the platform to be able to work with solvents and chemicals that are corrosive, volatile, or strong solvating agents for typical plastics. These improvements aim to reduce wear and tear, extend the lifespan of critical components, and ultimately ensure the platform's reliability for long-term use in high-throughput nanoparticle synthesis.

There is an existing ideology prevalent in our culture that radicalized, and gendered subjects are expected to endure copious amounts of pain when it pertains to their menstrual cycles. I call this into question and aim to explore alternative methods of alleviating dysmenorrhea beyond hormonal contraceptives and SSRIs. Focusing specifically on BIPOC menstruating populations, I have been the primary investigator of a study examining the effects of community dance and affinity spaces on menstrual pain management. Participants come into the dance studio weekly to engage in various open dance practices with others, in addition to journaling, guided massage, and discussion. The dance practices range from traditional Chinese practices like Qigong to local community dance practices like Dance Church. In addition to weekly sessions, I host quarterly BIPOC Jams open to the public, to share the knowledge with the wider community, cultivating a space for BIPOC to engage in freedom dreaming, community building, and collective healing. I will explore what a future of community healthcare would look like, moving away from Western models of healthcare that focuses solely on the individual. Drawing from practices like community acupuncture where the healing experience happens with others rather than in isolation, I am curious to investigate how having a shared dancing experience impacts and shifts the emotional and physical well-being of participants. I am exploring the care relationships that form in BIPOC affinity spaces and how dance as a language facilitates a different type of embodied healing. I will be presenting the structure that I have used for weekly sessions and the BIPOC Jams. I will also share excerpts of participant experiences and reflections from both spaces. I am drawing upon existing theories around care work, somatic abolition, and pain management to develop a practice of community care that builds upon existing discourse. 

Traumatic brain injury (TBI) results from a blow to the skull that causes shearing forces in the brain. Elevating intracranial pressure (ICP) at the moment of impact may protect the brain from TBI by stiffening the brain tissue and decreasing shearing. When they expect an impact, humans naturally brace and perform a Valsalva maneuver (exhaling against a closed airway), which momentarily elevates ICP. In a ferret TBI model, we conducted abdominal compression using a blood pressure cuff to induce a Valsalva-like response (VLR) and determine whether VLR resulted in neuroprotection. The ferret model was chosen for its gyrified brain structure and white to grey matter ratio that closely resembles the human. TBI was induced using a CHIMERA (Closed-Head Impact Model of Engineered Rotational Acceleration) device, which is designed to deliver high-energy, controlled skull impacts. Initial work showed that the abdominal compression procedures increased ICP. The TBI study involved a total of 36 adult ferrets of both sexes randomized into three groups: (1) a sham control group exposed to isoflurane with a cuff but no compression, (2) a TBI group with a cuff but no compression, and (3) a TBI group with a cuff and abdominal compression. Baseline behavioral assessments (CatWalk, Novel Object Recognition, Swim Test, and Open Field) were conducted one week prior to injury. Post-injury behavioral testing, using the same assessments, was performed at 24–48 hours and 8 days post-TBI to evaluate functional outcomes. On day 8, ferrets were euthanized, and their brain tissue was collected and assessed for neuropathological outcomes. We hypothesize that abdominal compression will mitigate deleterious TBI outcomes. If these findings are supported, this intervention could improve the lives of those at risk of TBI and contribute to ongoing research in the field.

Individuals with Stage II/III severe periodontal disease were recruited from the Graduate Periodontics Clinic at the University of Washington School of Dentistry using an approved IRB (STUDY00016871). Subgingival plaque samples were collected from four tooth sites: an active inflamed site, two adjacent tooth sites, and a distant healthy tooth site. Sterile paper points were inserted into the gingival sulcus for 30 seconds. DNA was isolated and extracted using the Qiagen AllPrep DNA/RNA Mini kit (Cat. #80204), then purified and concentrated using the Zymo Clean & Concentrator (Cat. #D4014) kit. 16S rRNA libraries were generated and sequencing was performed on the MiSeq platform (Illumina, San Deigo, CA, USA) using 300bp paired-end chemistry. Raw reads were processed and analyzed using Qiime2 and the DADA2 algorithm to generate amplicon sequence variants (ASVs), which were then classified using the expanded Human Oral Microbiome Database (eHOMD). Differences between tooth sites were assessed within and across individuals. Correlation between taxonomic levels and clinical data was also assessed. Data analysis is still being performed at this time. Based on previous literature (Pawolski et al, 2005, Kerns et al. 2023), we expect that a subgingival community gradient radiates from tooth sites affected with periodontal disease toward distant healthy sites. We aim to resolve this within individuals using ASVs for the first time. Additionally, we anticipate an increase in disease-associated bacteria within actively inflamed tooth sites, such species within Porphyromonas, Tannerella, and Treponema genera. Furthermore, we anticipate a gradient of perio-pathic disease-associated bacteria will decrease in relative abundance the further away from active diseased sites. We expect that results from our study will highlight the presence of a subgingival microbiome composition and enrichment of specific gram negative perio-pathic disease-associated species within clinically healthy tooth sites in patients with active periodontal disease despite the absence of clinically observed inflammation.

Cortical tracking, a method that examines how neural activity encodes the dynamic features of the incoming speech stimuli, allows for the study of naturally produced continuous speech. Successful encoding of acoustic features is fundamental for language processing and comprehension. Studies show that cortical tracking of at least some acoustic speech features is already robust in the first year of life. However, it is unclear whether bilingual infants exhibit enhanced cortical tracking of non-native languages compared to monolingual infants, consistent with the idea of having a "bilingual advantage" as suggested in prior research. To investigate this, we recorded neural responses from 11-month-old English learning monolinguals, English-Mandarin learning bilinguals, and two mature comparison groups of English monolingual and English-Mandarin bilingual adults, while they listen to naturally produced, continuous, infant directed speech using electroencephalography (EEG) in three conditions: English, Mandarin, and Vietnamese. Stimuli were presented at an overall level of 70 dB SPL in a sound-attenuated booth. Using a combination of machine learning and linear modeling (i.e., Multivariate Temporal Response Function approach), we analyze the EEG signals using a multivariate encoding model consisting of acoustic features including envelope, envelope derivative, word onset, and phoneme onset. We hypothesize that both bilingual adults and infants will exhibit enhanced encoding of acoustic features in Vietnamese compared to monolingual adults and infants, indicating bilingual advantage in processing a third language. Additionally, we anticipate the bilingual advantage to be more prominent in infants than adults. These findings will contribute to the understanding of how bilingualism influences neural encoding across different languages and provide neural evidence of bilingual advantage in processing and acquiring a third language. I participated in study design, recruitment, data acquisition and analysis.

The activation of inflammasomes is a crucial component of the early immune response to pathogens and initiates a form of inflammatory programmed cell death called pyroptosis. During infection, a cytosolic inflammasome-forming protein sensor detects a pathogen to assemble the inflammasome complex, which subsequently activates the protease Caspase-1 (CASP1). CASP1 processes Gasdermin D (GSDMD), inducing pyroptosis through pore formation in the plasma membrane, while also facilitating the release of proinflammatory cytokines, such as IL-1β and IL-18. Adenovirus (AdV) is a common pathogen that causes inflammatory symptoms by infecting multiple mucosal epithelial tissues in the respiratory tract and intestinal tract such as the nose, mouth, and eyes. We wanted to test whether AdV infection could activate one of the main inflammasome sensors in human conjunctival epithelial cells (hCjE cells), which is NLRP1. However, we found that upon AdV infection, NLRP1-mediated cytokine release is absent, suggesting that CASP1 signaling is suppressed. Interestingly, despite the loss of IL-1β and IL-18, pyroptosis remains unaffected. Recent studies indicate that in the absence of CASP1, inflammasomes can activate Caspase-8 (CASP8), leading to the cleavage of Caspase-3 (CASP3) and Gasdermin E (GSDME), resulting in an alternative, incomplete form of pyroptosis. Thus, I hypothesize that during AdV infection, host cells are still able to induce pyroptosis by activating the alternative CASP8-GSDME pathway. To test this hypothesis, we generated and validated genetic knockouts of CASP8, GSDMD, GSDME, and CASP3 in hCjE cells to assess their roles in pyroptosis during AdV infection. These findings will provide new insights into viral immune evasion strategies and inflammasome regulation in epithelial cells.

This study investigates the mechanical properties of A500-C steel round hollow structural sections through tension testing of coupons cut from tubes with various radii and thicknesses. Testing was conducted following ASTM A370 standards to evaluate relationships between carbon equivalent, strength ratios, and ductility. The carbon equivalent was determined using the International Institute of Welding equation with chemical compositions obtained from mill certifications. Strength ratios that were analyzed include measured tensile-to-yield strength, measured-to-mill certification values, and measured-to-nominal values, with comparisons to the ratios prescribed for design in the American Institute of Steel Construction Seismic Provision. The results indicate that most strength ratios and ductility metrics showed no significant correlation with HSS thickness or carbon equivalent. However, some trends were observed. Negative correlations were found between the ratio of measured to nominal ultimate strength and thickness, the measured tensile-to-yield strength ratio and thickness, the ratio of measured to mill-certification yield strength and carbon equivalent, and the ratio of measured to nominal yield strength and carbon equivalent. A positive correlation was observed between the measured tensile-to-yield strength ratio and carbon equivalent. These findings help provide insight into the variability of A500-C steel properties and their dependence on chemical composition and wall thickness, with potential implications for design assumptions in the structural design code.

Recent research shows the lux operon utilized with in-vivo bioluminescence imaging to detect infectious diseases in animal models. Modifications to this operon led to the development of enhanced bioluminescence in Escherichia coli cells. However, expression of this operon has not been optimized for expression in other bacteria, such as Staphylococcus aureus. This study aims to optimize the lux reporter gene expression for Staphylococcus aureus, so luminescence is bright enough to register without specialized equipment. To date, the research has explored Gibson Assembly for cloning the gene sequences into a shuttle vector and efforts to modulate gene expression to reduce toxicity in E. coli.

Silica nanoparticles have diverse applications in catalysis, imaging, and drug delivery. Tailoring these nanoparticles for specific applications requires precise control over their size, surface chemistry, porosity, and polydispersity. These properties are controlled by a wide range of factors such as reactant type and concentration, pH, reaction temperature, and other synthesis parameters. Due to the large parameter space, determining the optimal reaction conditions for synthesizing silica nanoparticles with the desired size and morphology is time-consuming and challenging. An accelerated experimentation platform integrating automation and artificial intelligence can streamline the selection of reaction parameters for synthesizing silica nanoparticles with targeted size and morphology using machine learning-based iterative design of experiments to optimize material properties. This system uses the Science Jubilee flexible laboratory automation platform to carry out sol-gel synthesis. Small-angle X-ray scattering is used to characterize the sample. The data collected is used to optimize the reaction condition for synthesizing the targeted nanoparticle. We have successfully carried out sol-gel processes and synthesized silica nanoparticles with various sizes and polydispersity using the platform. Currently, we are working on optimizing the selection of sample synthesis conditions.

Parents play a significant role in shaping adolescent alcohol use. The specific role of adolescent decisional freedom—the extent to which adolescents independently make decisions— has yet to be examined. I conducted a brief literature review on adolescent decisional freedom, and this study explores its links with alcohol use within distinct developmental periods. Data from baseline to year 6 follow-up of the National Consortium on Alcohol and NeuroDevelopment in Adolescence study (N=831) were tested for cross-sectional associations between decisional freedom and alcohol use phenomenology (i.e., drinking days per average month, past month alcohol consumption, quantity of drinks during average drinking period, and binge drinking days in the past year and month). Separate models were tested for early adolescence (ages 12-14), middle adolescence (ages 15-17), late adolescence (ages 19-20), and emerging adulthood (ages 21-24). Adolescent decisional freedom was measured using a self-report 5-point Likert scale across distinct domains (e.g., spending money, drinking alcohol, time spent with friends). Gender and age of first drink were covariates, and each model examined associations between decisional freedom and gender. Regression results consistently linked lower decisional freedom to lower alcohol use across all phenomenology in early adolescence (bs ≤ −.41, ps < .01). For middle adolescence, the protective effect of limiting decisional freedom only emerged for drinking days per average month (b = −.29, p < .01) and quantity of drinks during average drinking period (b = −.46, p = .001). In early and late adolescence, the association between lower decisional freedom and fewer past month binge drinking days was stronger for boys (bs ≥ 0.43, ps < .05). These findings suggest that increasing control over early adolescents’ decisional freedom, particularly for boys, and flexibly granting greater decisional freedom over time may protect adolescents from harmful decisions associated with alcohol use.

Kappa opioid receptor (KOR) ligands have been explored for anti-anxiolytic, anti-depressive, pain, and substance use disorder therapeutics. These therapeutic effects are partly due to biased signaling through the cJun N-terminal Kinase (JNK) pathway, which involves complex molecular interactions and downstream effects that inactivate the receptor by producing reactive oxygen species (ROS). JWT-101, a clinically approved compound, has been shown to produce therapeutic effects for these conditions. We hypothesize that its mechanisms of action are through KOR antagonism. I previously assessed KOR agonist-induced analgesia by measuring the latency of tail withdrawal from 52.5°C water after treatment with U50,488, a KOR agonist. Pretreatment with 15mg/kg JWT-101 24 hours before U50,488 injection effectively blocked KOR-induced analgesia in wild-type male mice. This effect was reversed by the short-acting, KOR-selective antagonist Aticaprant (5 mg/kg), suggesting that JWT-101’s action is mediated through KOR. Further investigation using in-vivo fiber photometry with the novel peroxide sensor AAV oROS-Gr revealed that JWT-101 significantly increases ROS production in KOR-expressing cells. Injection of 15 mg/kg of JWT-101 increases oROS fluorescence compared to control post-injection. Pretreatment with Aticaprant 15 minutes prior to JWT-101, blocks oROS fluorescence, suggesting that JWT-101’s activity is mediated by KOR. Pretreatment with MJ33 (a PRDX6 inhibitor upstream of JNK activity) 50 minutes before treatment with JWT-101 blocked oROS fluorescence, suggesting that this ROS production is through the JNK/PRDX6 pathway of KOR activation. This study provides insights into the mechanism of action of JWT-101 and examines the underlying molecular mechanisms of KOR-associated effects.

This project aims to compare and contrast Little Free Pantries (LFPs) and Community Fridges (CFs) as models of micro pantries for those facing food insecurity. The primary focus is on the ability of each to safely provide nutrient-dense food. There is extensive research on what a nutrient-dense diet is and its importance on a person's health as well as budding research detailing the quality of food provided by food pantry organizations. However, this research is limited in the scope of donation programs being researched. Furthermore, there is a lack of understanding how different donation programs differ in their ability to provide nutritional food to those utilizing their services. This project compares five CFs to five geographically matched LFPs within the City of Seattle. To assess the nutrient-density of food donated to CFs and LFPs two dimensions of food nutrition are analyzed utilizing the FAST score and NOVA categorization methodologies. Each micro pantry is briefly assessed on its food safety standards as well. CFs are expected to provide food with higher nutritional quality than LFPs, and in a safer manner. This is due to their ability to be temperature controlled, allowing for a wider variety of foods to be collected and stored safely. This research will be presented in a final paper and poster detailing the findings of the project as well as any recommendations drawn for the City of Seattle. This project is significant because it addresses the nutrition of food made available to those facing food insecurity. Understanding the difference in quality of food offered between the CFs and LFPs will allow for an assessment regarding how accessibility to nutrient dense food for all residents of Seattle falters and how it can be improved.

Human gastrulation is the period of embryonic development during which a single-layered blastula develops the three germ layers, which give rise to all of the specialized cell types in our bodies. Differentiation of these layers is controlled by epigenetic factors, which chemically modify the DNA, therefore activating or repressing a gene’s activity. Very little is known about the role of epigenetic factors in human gastrulation, as it’s difficult to obtain samples at the proper time for study; samples from IVF are too early to study, and fetal samples are too developed. Despite these complications, it’s important to study gastrulation because it’s during this time that developmental disorders and loss of pregnancy can occur. My goal is to delete seven epigenetic factors and determine their role in human embryogenesis using a human pluripotent stem cell derived embryoid model (retinoic acid treated gastruloids). Using CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 technology, I plan to perform individual gene knockouts on our genes of interest in human embryonic stem cells. Next, we will generate mutant gastruloids from these knockout cell lines, and phenotype using single-cell RNA sequencing and fluorescent microscopy. From there, we can see how knocking out this gene affects gastruloid cell type composition and morphology. Using this strategy, our lab has successfully knocked out 60 genes. Given the strong phenotypes observed in null mutant mouse embryos for these genes, we expect to observe strong phenotypes from these seven epigenetic factors. With these findings, we can further understand the role of these epigenetic factors in development and disease. These findings can advance the progress of therapies and better understand our knowledge of human embryonic development as a whole.

The Campanian stage of the Late Cretaceous (84–72 million years [Ma]) was a dynamic interval for North American ecosystems and included the zenith of dinosaur diversity and the regression and transgression of the Western Interior Seaway (WIS). Most studies that investigate vertebrate biodiversity during this interval focus on dinosaurs, whereas few focus on changes in herpetofauna (lizards, frogs, and salamanders). Herpetofauna are important indicator species of ecosystem dynamics, because they are fragile to ecosystem change. Vertebrate microfossil sites are ideal for studying herpetofauna diversity dynamics through time because they can produce large sample sizes, sample aquatic environments, and are plentiful through stratigraphic intervals. The Judith River Formation (JRF) of north central Montana is rich in vertebrate microfossil sites, preserving ~4 Ma of the Campanian (~79–74 Ma). Here we aim to document patterns of herpetofauna diversity change in the JRF by quantifying herptile taxonomic richness and relative abundances using specimens from three temporally separated microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (76.5 Ma), and Clamfetti (~75.2 Ma). We collected sediment samples from these sites over four years and processed them via underwater screen-washing techniques. Presently we have studied 470 herptile microfossils (600 planned). Our preliminary results show changes in the taxonomic diversity across the sampled sites. Taxonomic richness of herptiles varies through the formation, first increasing and then decreasing. Salamanders have the highest relative abundance, lizards decrease in relative abundance, and frogs fluctuate. We hypothesize that taxonomic patterns are influenced by the impact of WIS cycles on water supply in ecosystems: amphibians thrive in wetter environments, whereas lizards are more terrestrial. These preliminary results reflect a connection between diversity patterns and extrinsic drivers not observable through the analysis of dinosaur fossils. Our continued analysis will provide more fine-scale resolution of herptile diversity during the Campanian.

Substance use in Indigenous communities remains a significant public health concern for Indigenous communities worldwide, greatly affecting physical, mental, and social well-being. Substance use in Indigenous communities is nearly double that observed in the non-Indigenous population (Geia, et al., 2018). Such prevalence of substance use among Indigenous populations has been a source of stigma greatly related to colonialism. This study examines the prevalence of substance use among Indigenous populations in Australia, New Zealand, Canada, and the United States identifying patterns within communities and successful intervention strategies to decrease substance use in these communities. A systematic review of literature conducted in the countries mentioned above reveals that Indigenous communities experience high rates of alcohol, tobacco, and illicit drug use. Secondary to trauma and socioeconomic disparities paired with limited access to secular healthcare contributes to the exacerbation of the cycle of addiction (Spillane, et al., 2023). Specific led interventions sculpted around Indigenous culture and various community-driven, utilised participatory approaches show a high chance of decreasing substance use in these communities (Geia, et al., 2018). With such findings, the need for healthcare services that remain respectful to Indigenous culture and overall strengthen community engagement can be put in place to mitigate the prevalence of substance use in these communities and the corresponding risk factors that contribute to such circumstances. My presentation will demonstrate how the high levels of alcohol and substance use can be reduced in Indigenous communities when ethical interventions are implemented that provide long-term care for rehabilitation. This long-term care should include education, harm reduction, and encouragement for partnership between Indigenous individuals and their families and healthcare providers within the programs. The long-term care is to be residential to those struggling with substance use, rather than mainstream outside of reservations, to ensure the patients feel safe.

Behavioral flexibility is the ability of an animal to adapt to environmental changes, crucial decision making and goal directed behaviors. Impaired behavioral flexibility has been linked to psychiatric disorders such as depression, anxiety, and substance use disorders. Emerging research suggests that psilocybin, a psychedelic drug that acts on serotonin receptors, may improve behavioral flexibility by promoting adaptability in responses to new information. Given the growing literature exploring the impact of psilocybin as a therapeutic treatment for psychiatric disorders, this study aims to explore the effects of psilocybin on the use of behavioral strategies on a complex spatial set-shifting task. Long-Evans rats were trained on an elevated plus maze with two start arms, north and south, and two reward arms, west and east. The task requires rats to alternate between two strategies: alternation and place. The alternation phase required rats to switch between reward arms (go West, then go East), and the place strategy required choosing the same arm (e.g. go West) continuously. Rats must determine the correct strategy and implement it; once 12 out of 15 trials are accurately completed, an uncued switch in the correct strategy will occur, requiring adaptation to a new strategy. Once animals were well-trained on the task, a single dose of psilocybin (1mg/kg) or saline was administered 10 minutes prior to a session and their behavior was analyzed. Metrics such as performance, and flexibility scores were assessed to determine the impact of psilocybin on behavior. Preliminary findings suggest psilocybin improves behavioral flexibility compared to the saline group, though overall performance remains relatively stable. These results provide insight into the potential of psilocybin as a therapeutic tool for conditions characterized by behavioral rigidity; even in wild-type animals, psilocybin improves flexibility, indicating the possibility for mitigating more severe impairments in flexibility seen in psychiatric disorders.

Adaptive algorithms used in brain-computer interfaces (BCIs) adjust to user strategies by dynamically adjusting how BCIs decode neural data throughout an experiment. Current adaptive algorithms continuously update the decoder using all available data during training. However, if users are unfocused or inattentive, it is likely that some of the training data is unhelpful towards decoder training and could lead to poor decoder performance. Unfortunately, determining attentiveness in a subject is difficult. Non-human animals cannot self-report attention levels, and even in human trials, self-reporting often leads to subjective data that varies between subjects. A non-invasive estimate of subject attentiveness could improve data selection for decoder training. Pupil size is correlated with a participant’s perception of task difficulty, and participants involved in attention-grabbing tasks display blinking rate-inhibition (Kucewicz et al., 2018; Maffei et al., 2019). I hypothesize that these eye data could be used to estimate a subject’s task engagement. I explored data from a novel task where both human and non-human primate subjects controlled a cursor on a 2D screen with 3D hand motions through some unknown mapping. Due to the unknown 3D-to-2D mapping, this task required constant cognitive attention in order for subjects to succeed. I looked at the subjects’ data to identify trends in pupil size and blink frequency across multiple days of task performance. In the future, I aim to build engagement classification models to better select training data for adaptive algorithms and apply these algorithms to realtime BCI experiments.

South Thurston County's car-dependent and low-density built environment can affect the health and economic wellness of its residents. This research investigates the barriers that residents face in getting to work, their daily needs, and things-to-do. What are the best strategies to improve the built environment that provides access to employment, necessities, and entertainment for people in south Thurston County’s SR 507 and Old Highway 99 corridors? A process of observations, community surveys and interviews with government and other agency officials will allow for an understanding of current conditions in the study area, personal viewpoints of community members, and constraints that the government agencies and other organizations might face in making improvements. This project will include investigation into design, policy and economic practices. A free or low-cost guide that would allow rural governments to make economically smart design and planning changes, and help make towns more self-sustainable, will be created after understanding this research. As innovation in planning and re-urbanization occurs increasingly in the United States’ larger metropolitan areas, rural and tribal communities, too, deserve an opportunity at urban core making, simplifying the daily lives of its residents, and maintaining health and wellness for all.

Chloroplasts are central to plant immunity and act as a hub for immune signalling and defence-related hormone synthesis. The essential chloroplast-localized protein FtsHi1 is a component of the FtsHi import motor and is vital to translocating proteins across the chloroplastic membrane. Viral-induced gene silencing (VIGS) of FtsHi1 in Nicotiana benthamiana results in a bleached phenotype, indicative of decreased translocation of essential chloroplastic proteins and decreased chlorophyll synthesis. Previous work identified herbivore-induced kinase 1 (HIK1) as a potential interactor of FtsHi1. HIK1 is a receptor-like cytoplasmic kinase (RLCK) implicated in the immune response to caterpillars. FtsHi1 contains a predicted RLCK phosphorylation site, indicating possible phosphorylation of FtsHi1 by HIK1, which could promote defence signalling over photosynthesis. This project aims to test the impact of phosphorylation on FtsHi1 function and its role in protein translocation across the chloroplastic membrane. This work utilises engineered FtsHi1 variants, which mutate the serine phosphosite to either mimic FtsHi1 phosphorylation (Ser→Asp), prevent it (Ser→Ala), or recapitulate the wild-type protein sequence. To test the phosphosite mutation effects, FtsHi1 VIGS knockdown of N. benthamiana leaves will be transiently modified using Agrobacterium tumefaciens bacteria to express WT or phosphorylation-modified FtsHi1 constructs. The resulting colour phenotype for each construct will then be compared to the bleached phenotype of TRV2:FtsHi1 plants and the phenotype of wild-type plants. I hypothesise that the FtsHi1 phospho-null mutant will result in a rescue phenotype similar to wild-type FtsHi1, whereas FtsHi1(phospho-mimic) will retain the bleached phenotype.Examining FtsHi1 phosphorylation enhances our understanding of its potential interaction with HIK1 in herbivory-induced plant defences. Future studies will explore FtsHi1's role in defence mechanisms, with implications for engineering herbivory-resistant crops. 

Prostate cancer has a significant heritable component. It is estimated that 10-15% of patients with advanced prostate cancer carry an inherited predisposing genetic mutation, and these patients generally present with a younger age of onset and a strong family history of cancer. The standard in the field of oncology is to conduct short-read DNA sequencing on such patients to find predisposing mutations. While short-read sequencing does well to identify simple mutations that cause disease in many families, our lab concluded that short-read sequencing misses critical mutations in many prostate cancer susceptibility genes. We hypothesized that prostate cancer in many families is due to complex inherited mutations such as genomic deletions, inversions, and mobile element insertions that are not detectable by conventional genomic technologies such as short-read sequencing. To test this hypothesis, our lab specifically recruited prostate cancer patients who, despite having family histories of cancer, did not have any mutations detected via conventional genetic sequencing methods. This project utilizes Nanopore long-read DNA sequencing, which reads DNA in longer fragments and can reliably detect complex mutations. My role is to conduct long-read sequencing on DNA samples from these patients, then analyze the DNA sequence for mutations. I have sequenced 32 patients so far and identified 4 complex mutations through long-read sequencing which were missed by other approaches. These complex mutations include insertions of repeat sequences and duplications which disrupt gene function in BRCA1 and BRCA2. This suggests that, consistent with our hypothesis, some patients who do not have mutations found via conventional sequencing methods do indeed carry causative mutations in well-established prostate cancer risk genes. By finding these mutations, patients can receive more targeted and effective cancer treatment, and undiagnosed family members stand a better chance of catching cancers at earlier stages.

The Kodiak Archipelago in southern Alaska has a rich archaeological heritage that has fascinated archaeologists and local communities for decades. Despite the presence of many archaeological research projects, archaeobotanical remains found during excavation have yet to be analyzed. The archaeobotanical remains recovered from the Kodiak Archipelago have often gone overlooked by archaeologists who considered preservation too poor in the wet climate and focused instead on fauna from shell-midden sites or other cultural artifacts. The Tanginak Spring site on Sitkalidak Island in southeast Kodiak was excavated by University of Washington field schools between 1994 and 2003. It is considered one of the oldest identified sites on the archipelago, dating to 7500-6000 cal BP. Sediment samples taken during these excavations were retrieved, floated, sorted, and identified by the archaeobotany class at the University of Washington. This poster presents the initial results of the analysis of wood charcoal and other preserved plant remains from the site, providing evidence to develop new insights into plant use by Kodiak’s earliest settlers.

The proximal tubule (PT) and glomerulus are vital blood-filtering components of the nephron, the functional unit of the kidney. The components’ micro-scale sizes and intricate three-dimensional structures are critical to kidney function, although accurate in vitro modeling has proven difficult. Limitations in fabrication techniques have forced size scaling and imprecise morphology in models. In this study, we addressed fabrication limitations using multiphoton ablation to etch intricate, three-dimensional proximal tubule and glomerulus vessels in collagen hydrogels. We sought to demonstrate model viability by introducing human proximal tubular epithelial cells (hPTECs) and human umbilical vein endothelial cells (HUVECs), respectively, through cell perfusion. However, we encountered a significant challenge: due to the small diameter and high curvature of the micro-scale channels, the cells tended to aggregate, disrupting cell profusion and cellularization throughout the vessels. Cell aggregation was especially prominent in the glomerulus model due to the more tortuous and complex geometry. While our cellularization trials on native-scale models proved it is feasible to perfuse cells throughout the vessel, we still need to refine cellular profusion and cellularization. To improve cellular profusion and cellularization, we are first studying a 1.5-scale glomerulus model. The scaled model's increased vessel diameter and lower curvature demote cell aggregation and enhance the ease of cell profusion. We anticipate that cellularizing the 1.5-scale model will provide a deeper understanding of the variables facilitating cell profusion that we can use to improve native-scale vessel cellularization. Fabricating native-scale, accurate in vitro PT and glomerulus models is crucial for developing a deeper understanding of hemodynamic influence on kidney function. These findings contribute to the fabrication of more biomimetic in vitro PT and glomerulus models that will pioneer therapeutics and the understanding of kidney physiology and pathology.

Since the discovery of DNA in the 19th century, biochemists have been elucidating not only the structure, but unique biochemical environment of each loci. Protein-DNA neighborhoods govern chromatin structure and cellular functions (transcription, replication, etc.). To investigate which proteins and oligonucleotides compose these microenvironments, our lab and collaborators developed DNA oligonucleotide-directed proximity-interactome mapping (DNA O-MAP), a locus purification method using oligo-based ISH probes to recruit horseradish peroxidase (HRP) activity to specific DNA intervals (Liu & McGann et. al. 2024). Once these secondary, HRP-conjugated probes are localized to loci of interest, hydrogen peroxide is added with biotin-tyramide. Hydrogen peroxide activates HRP, forming biotin-tyramide phenoxyl radicals that biotinylate proteins and nucleic acids within 10-75nm. This allows for a scalable, versatile method to investigate these microenvironments. Large scale DNA O-MAP, tiling across several genomic sites, can elucidate insights into biological questions. However, the upstream protocol remains a barrier to its throughput, sensitivity, and reproducibility. In order to ensure this for analysis of tagged proteins, we sought to automate the streptavidin affinity purification protocol onto the Opentrons OT-2 robot. This is where streptavidin-coated magnetic beads capture biotinylated species from lysate. Coupled beads are recaptured with a magnetic rack and pipetting-off of flow-through. Subsequently, several washes cleans up these beads before peptides are digested off via Trypsin/LysC, dried-down, resuspended, and loaded onto a Orbitrap Eclipse LC-MS for proteomic analysis. Purification of streptavidin beads is manually intensive, inherently leading to variation between runs. The Opentrons OT-2 is an open-source liquid handler, allowing our lab to easily transfer methods to others interested in DNA O-MAP. Automating this protocol launches us from technology development to biological application. Here, I present an automated protocol for streptavidin affinity purification and evaluation of its effectiveness via comparison of the automated protocol to our lab's current, manual methods.

Understanding the ecology of vegetation systems in Earth’s past in response to past warming events helps contextualize how they might respond to current climate events. Ecological succession is an ecosystem dynamic in which plant species with different life strategies replace each other as plants colonize a disturbed habitat. Reconstructing which successional stage a fossil plant represents is an important step in reconstructing this process in the past. However, fossil plants preserve a limited number of traits. Leaf vein density (LVD) is a trait that relates to maximum photosynthetic rates and can be measured from fossil leaves, but there is limited empirical evidence for how it varies across succession in temperate deciduous forests. To address this knowledge gap, our study measures LVD of modern plant communities across a successional gradient in western North Carolina. We hypothesize that plants in younger forests have greater access to sunlight due to a less established canopy and will therefore have higher LVD to support a higher photosynthetic rate. As succession progresses and the canopy closes, we hypothesize that LVD will decrease with reduced light availability. Samples were taken from five sites in western North Carolina that vary in how long forest re-growth occurred following clear-cut timber harvesting, 4, 21, 44, 94, and roughly 200 years. At each site, leaves were collected and sampled at a community scale and were chemically treated to create images that highlight the veins. We then used ImageJ to measure LVD. The community mean and variance of LVD across succession will be analyzed, using both unweighted and weighted approaches, to test our proposed hypothesis of decreasing LVD through succession. Preliminary results suggest a potential LVD decrease as hypothesized but driven more by understory species rather than dominant tree species. Future work will refine interpretations and consider implications for the fossil record.

In the wake of the Trump and Biden administrations, during which movements such as Christian nationalism and religious deconstruction brought civil religion into the public eye, scholarship regarding religion as it interacts with politics becomes increasingly relevant. My thesis aims to investigate the role of Christianity in the political communication of our two most recent presidents, arguing that public religiosity is not diminishing in America -- rather, it is in a constant state of evolution to fit an ever-changing nation. This content analysis compares Trump's and Biden's usages of Christian language to one another as well as to former presidencies, addressing the question of how religious rhetoric is shifting in American political discourse. Through creation of a codebook of more than one hundred Christian keywords, which are then applied to presidential communication such as State of the Union addresses (accessed through The American Presidency Project), I determine the frequencies and contexts of religious mentions within Trump's and Biden's communication. Using programs such as Atlas.ti, I measure, analyze, and visualize Trump's and Biden's individual invocations of Christian talk. I hypothesize that Donald Trump's use of religious language increased over the course of his presidency as well as being significantly concentrated in self-referential contexts. Meanwhile, Joseph Biden's religious language is expected to be concentrated in contexts of national crisis, mainly taking the form of Biblical quotations. Overall, findings are expected to demonstrate that Christian language in the American presidency is not broadly declining, but rather used in more niche contexts. This project contributes to the vast field of religious and political scholarship by comprehensively analyzing not just the frequency but also the context of religious language in these presidencies, supporting the notion that public religion is a living entity that functions as a sociological and cultural phenomenon.

In Adoptive Cell Therapy (ACT), a novel modality of cancer therapy, immune cells can be engineered with T cell receptors (TCRs) to aid in targeting specific antigens presented on the surface of cancer cells. However, TCR-T cells often have limited persistence after transfer into patients, which has hampered the effectiveness of this therapy for solid tumors. Last year, our lab identified LSD1 as a target for drug inhibition, which is an enzyme that alters the epigenome of cells via histone modifications. My project aims to understand the mechanism of LSD1 inhibitor drugs, as well as the effect of these drugs on two types of T cells: cytotoxic CD8+ cells and helper CD4+ cells. In addition to understanding how LSD1 drugs work, I also ask exactly how CD4+ cells enhance the function of CD8+ cells in tumor killing. Which receptors on CD8+ cells are activated by helper T cells, what is the signal phosphorylation pathway transducing the "helping" signal from receptors, and what downstream epigenetic regulators play a role in translating the "helping" signal into better function in CD8+ T cells? To assess these interactions, I will generate a diverse population of CD8+ T cells with targeted receptor knockouts, known as a receptor library. Similar libraries will be generated for epigenetic regulators as well as kinases/phosphatases. The performance of T cells will be assessed via coculture assays, where T cells can kill tumor cells but not fully eliminate the tumor because of periodic addition of new tumor cells. At the end of the coculture period, we will assess gRNAs enriched in dysfunctional populations, which will identify genes critical to CD8+ T cell function. This project aims to provide enhanced function of T cells that are better suited for applications in clinic.

Unlawful behavior by both the government and its civilians in Mexico has developed into a crisis of violent crimes and corruption. There is a culture of high disregard of the law that is fueled by distrust in the government, subcultures such as Narco-culture, as well as institutional weakness. The aims of this study are to learn of the experiences Mexican citizens have with unlawful behavior and corruption in their government as well as understand the motivations behind this kind of behavior. For the purpose of this study, unlawful behavior will be defined as any behavior or action that violates Mexican law. Through semi-structured interviews of adult Mexican citizens I will gain insight on their thoughts and experiences. They will be asked questions regarding their participation and experiences with unlawful behavior. Due to travel limitations, the Mexican citizens interviewed for this study will be residents of Washington state. It is Mexican citizens that are facing the consequences of the high crime and corruption which makes it imperative to amplify their stories and understand their experiences and perceptions. The information collected through this research may aid in finding a solution to Mexico's crisis of crime and corruption in hope of providing Mexican civilians with a better quality of life. 

Acetaminophen (APAP) is a widely used over-the-counter drug known for its analgesic and antipyretic properties. Several clinical factors can influence how APAP is absorbed, distributed, metabolized and excreted from the body (i.e., its pharmacokinetics (PK)). APAP is metabolized into several metabolites, including APAP-glucuronide, APAP-sulfate, APAP-cysteine, and APAP-N-acetylcysteine. Therefore, accurately determining plasma concentrations of APAP and its metabolites is crucial for understanding how individuals metabolize APAP and environmental influences on APAP PK. To address this, I am reproducing a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay to determine concentrations of APAP and its metabolites in plasma. I analyzed plasma samples collected from seven healthy volunteers following oral administration of 500 mg of APAP. To prepare the samples, I added 70 μL of diluted internal standard mix into the tubes containing 30 μL of plasma. Samples were centrifuged and the supernatants were transferred clean tubes and dried down with nitrogen gas. Samples were reconstituted in mobile phase for analysis using LC-MS/MS. I analyzed the LC-MS/MS data to calculate the plasma concentration vs. time curves for each analyte. I used Phoenix WinNonlin to estimate key PK parameters, including peak concentration (Cmax), time of peak concentration (Tmax), clearance, half-life, volume of distribution, and area under the curve (AUC). This LC-MS/MS assay provides a platform for precise quantification of APAP and its metabolites, and will be essential for our lab’s future studies on the impact of the gut microbiome on APAP’s PK.

The Aurignacian, a major cultural phase of the Upper Paleolithic, was characterized by remarkable advancement in the social and cognitive capacities of human beings. This period is marked by technical innovations - such as bone tools and weapons, and artistic developments - in the form of cave paintings and portable art. Evidence from this time period also suggests the emergence of social groups spread across Europe. We investigate interactions between these groups by studying the distribution of objects with engraved geometric signs. We use data from SignBase, a large catalog of archeological data from European Paleolithic sites to quantify group areas and site hierarchies, identifying potential ‘checkpoints’ and ‘central places’. Applying seriation, networks analysis, and measures of sign richness and diversity, we examine how the social dynamics change over the four sub-periods of the Aurignacian. We infer patterns of social group boundaries and interactions, improving our understanding of the structure and complexity of Aurignacian social networks.

The Campanian stage of the Late Cretaceous (~84–72 million years [Ma]) was a dynamic interval for North American ecosystems including the evolution of angiosperm plants and the regression and transgression of the Western Interior Seaway (WIS). These dynamics likely impacted terrestrial fauna across the continent. Most studies investigating biodiversity in western North America during the Campanian focus on a single group (e.g., dinosaurs or herpetofauna), whereas few investigate diversity patterns of multiple taxa. This approach is imperative because comparing diversity patterns among taxa can provide rare insight into the synecology of animal communities. Vertebrate microfossil sites are ideal for such a study because they preserve large sample sizes, multiple taxonomic groups that likely coexisted, information about environmental conditions, and they sample multiple stratigraphic intervals. The Judith River Formation (JRF) of north central Montana preserves ~4 Ma of the Campanian (~79–74 Ma) and large regressive and transgressive cycles of the WIS. This formation, which is contemporaneous with the Dinosaur Park and Two Medicine formations, is also rich in vertebrate microfossil sites. To examine vertebrate diversity patterns through this critical interval, we compared taxonomic richness and relative abundances of Dinosauria, Squamata, and Lissamphibia from the JRF from three temporally distinct microfossil sites: Makela-French 1 (~77.5 Ma), Milkshake (~76.5 Ma), and Clamfetti (~75.2 Ma). Over four years, we collected and screenwashed fossiliferous, bulk-sediment samples from these sites. Thus far, we have recovered 998 and aim to recover 1,200 specimens total. We use our data and knowledge from the literature to evaluate the extrinsic factors (e.g., seaway regressions) that drove diversity changes in the JRF fauna.  Our preliminary results suggest a connection between diversity patterns and WIS cycles. We observe shifts in relative abundances and richness near the onset of the WIS transgressive cycle. 

My project intends to discover a DNA aptamer, a single stranded DNA oligonucleotide, that binds selectively to the protein Interleukin-6 (IL-6). IL-6 has an important role in the immune system response and in excess it is known to cause inflammation. Aptamers exhibit binding affinities like that of antibodies but are ~50 times cheaper to produce. The method of aptamer discovery is through SELEX (Systematic Evolution of Ligands by Exponential Enrichment) which involves the selection from an aptamer library that contains 52N random nucleotide region and constant 5’ and 3’ 18 base pair regions for PCR amplification. Positive and negative selection are completed by incubating aptamer libraries with IL-6 or random protein immobilized on magnetic beads respectively. After each round selected aptamer sequences are amplified with a polymerase chain reaction (PCR) with primers that anneal to the constant regions. Reverse primer has biotin on 5’ end that is used later for strand separation with streptavidin agarose. After each round aptamer pool is going to be sequenced using nanopore sequencing platform till the enrichment of IL-6 specific sequences is observed. Binding will be tested through an enzyme-linked immunosorbent assay (ELISA) using the fam on 3’ end. The end goal of this project is to design a cost-effective method of IL-6 depletion from patients blood, allowing for cost-effective method of treatment for overactive immune system inflammation in sepsis patients.

During neonatal transport, specialized pediatric transport teams closely monitor the status of critically ill newborns. Hyperspectral imaging, a method of manipulating light for medical imaging, can be used for remote monitoring using video of the patient’s physical appearance and to measure vital signs. Appropriate light intensity is critical for clear visibility of the newborn and hyperspectral imaging accuracy, but this must be balanced with safety for sensitive eyes. My previous studies have determined the minimum range of light needed to accurately view the neonate in a transport incubator. My current research is focused on developing a novel method for vital sign analysis by using hyperspectral imaging. A smartphone camera will be used to take RGB photos of a calibration chart and a short video of the wrist of study participants. After taking the RGB photographs, custom MATLAB code will be used to extract physiological data such as hemoglobin and bilirubin content from the skin. Data analysis will compare the vital sign data collected using hyperspectral imaging and using a pulse oximeter to understand the feasibility of hyperspectral imaging for vital sign extraction. The expected result of this study is that the heart rate and blood oxygen levels measured using light and a pulse oximeter will be highly correlated. In conclusion, this research will demonstrate the potential application of hyperspectral imaging to pediatric transport.

Heart attack survivors experience elevated risk of subsequent events and death, as such there is a clinical need for regenerative techniques to rebuild damaged myocardium and reduce risk. Transplantation of human-induced stem cell-derived cardiomyocytes (hiPSC-CMs) into non-human primate hearts has been shown to significantly improve contractile function after heart attack, however, transplanted hearts were also shown to be at elevated risk for developing potentially lethal arrhythmias. Researchers developed a line of hiPSC-CMs to correct this arrhythmia-promoting behavior by inducing a series of four gene edits to prevent the hiPSC-CM spontaneous beating behavior known as "automaticity", these gene edits spawned the cardiomyocyte cell line dubbed MEDUSA (Modification of Electrophysiological DNA to Understand and Suppress Arrhythmia). I have conducted an in-vitro study of the electrophysiological effects of the MEDUSA edits, knockouts of the sodium-calcium exchanger NCX1, the hyperpolarization-activated pacemaker current channel HCN4, the low voltage Calcium ion channel Cav 3.2, as well as overexpression of the potassium channel Kir 2.1. I have employed immunofluorescence microscopy to analyze sarcomere structures, used lentiviral transduction of calcium-sensitive green fluorescent protein to quantify calcium handling, and constructed engineered heart tissue casts to measure contractile force, to compare the electrical and physiological characteristics of MEDUSA CMs and their wild-type counterparts. Characterizing the MEDUSA cell line is essential for identifying issues that could compromise the cells' ability to function in grafts while uncovering its potential for use in regenerative treatments. Here I show that the MEDUSA gene edits create arrhythmia-resistant cardiomyocytes without compromising the integrity of their structure or function, supporting the development of a regenerative therapy future for the field of cardiology.

Adoptive cell therapy with CAR-T cells has shown promise in hematological malignancies, but efficacy in solid tumors remains a challenge in part due to CAR-T cell exhaustion and antigen heterogeneity. However, the vast majority of preclinical models do not recapitulate the tumor-immune interactions that produce these barriers. To study CAR-T therapy in a rigorous model that recapitulates tumor-immune barriers, we adapted a Kras^LSL-G12D/+;P53^f/f (KP) genetically engineered mouse model (GEMM) of lung adenocarcinoma. However, adapting the KP-GEMM model for various target antigens, genetic drivers of disease, or interfacing with the vast array of powerful genetic mouse models is resource intensive which prohibits widespread utility. Here, we propose a defined, modular system for generating GEMM for CAR-T preclinical studies using the Sleeping Beauty (SB) transposon system. The proposed system uses polyethylenimine (PEI) to deliver SB transposon encoding oncogenic Kras^G12D and P53^R175H dominant alleles as well as our target antigen hROR1, in vivo to wild-type mice. We demonstrate that in vitro PEI successfully introduces genetic cargo into lung epithelial cell lines, while SB transposons mediate stable integration and expression. Next, we will test this in vivo. This system affords the induction of tumors with specific oncogenic driver mutations and specific tumor antigens on any genetic background. Ultimately, we expect that this approach will streamline preclinical use of GEMM in preclinical research. 

This project examines how industries' return-to-work policies influence public transit ridership patterns across various business sectors in the Puget Sound area. By analyzing ORCA card data from local transit agencies and reviewing company policies, the research tracks the impact of policy on industry ridership trends from January 2018 to January 2025, spanning the pre-pandemic, pandemic, and post-pandemic periods. The findings provide insight into industry-specific ridership changes, revealing which industries in the Puget Sound area have experienced the most significant shifts in public transit ridership post-COVID-19, and how return-to-work policies may have influenced these changes. The results of this research can be used by public transit agencies to focus and adapt their strategies to engage low-ridership sectors. This work can also help advance equitable, sustainable, and resilient public transit systems, particularly in the context of evolving remote work policies.

Malaria, caused by Plasmodium parasites and transmitted via mosquito bite, caused over 600,000 deaths in 2022, making the disease a pertinent public health problem. After injection into mammalian hosts through mosquito bite, Plasmodium parasites travel into the liver and develop in hepatocytes, where they undergo massive replication but cause no symptomatic disease. The parasites then egress into the bloodstream, where they infect red blood cells and cause the clinical symptoms and mortality associated with malaria, along with transmission to mosquitos to continue the cycle of infection. Although the liver-stage of the parasite is clinically silent, parasite infection of the liver results in incompletely understood hepatic immune responses that impact the development of immune memory, which is necessary for protection from future infections. Innate-like αβ and γδ T cells make up a significant proportion of intrahepatic lymphocytes, leading us to become interested in how these immune cells respond to a primary Plasmodium parasite infection of the liver. To address the role of these T cells in combating a primary liver-stage infection, we infected wildtype mice, mice that lack αβ T cells, and mice that lack γδ T cells with Plasmodium parasites and examined parasite density, size, and hepatic localization using immunofluorescence microscopy. Preliminary results demonstrate no significant differences in malaria parasite susceptibility between wildtype mice, mice without αβ T cells, and mice without γδ T cells, indicating that these cell types alone may not mount a significant anti-Plasmodium response upon primary infection. Future work will involve examining T cell localization within infected tissues to determine how T cell localization is impacted by primary infection and characterizing subsets of T cells that are present in infected livers. We hope these results add to a greater understanding of the entire hepatic immune response to primary Plasmodium parasite infection of the liver.

Individuals with Stage II/III severe periodontal disease were recruited from the Graduate Periodontics Clinic at the University of Washington School of Dentistry using an approved IRB (STUDY00016871). Subgingival plaque samples were collected from four tooth sites: an active inflamed site, two adjacent tooth sites, and a distant healthy tooth site. Sterile paper points were inserted into the gingival sulcus for 30 seconds. DNA was isolated and extracted using the Qiagen AllPrep DNA/RNA Mini kit (Cat. #80204), then purified and concentrated using the Zymo Clean & Concentrator (Cat. #D4014) kit. Whole genome libraries were generated and whole genome sequencing was performed on a NovaSeq X (Illumina, San Diego, CA, USA). Relative abundance of species-level assignments represented by clusters were determined, and best matched genomes were then used to generate species pangenomes for comprehensive multi-genome wide read mapping and gene-level analysis. Taxonomic and gene level functional analysis was also performed. Data analysis is still being performed at this time. Based on previous literature (Basic and Dahlén, 2023), we anticipate that the activity of certain microbial metabolic pathways associated with oral disease and their functions will be heightened in the active disease site and lower on the non-affected site within strain-level disease-associated bacteria, such as those of the Porphyromonas, Tannerella, and Treponema genera. Specifically, we expect amino acid fermentation and lipid metabolism activity to be increased in the active disease site. We expect that results from this study will highlight the presence of heightened activity of bacterial metabolic pathways and functions at the strain level associated with specific gram negative perio-pathic disease-associated species within clinically healthy tooth sites in patients with active periodontal disease despite the absence of clinical observed inflammation.

Cascadia Subduction Zone, a major fault off the Pacific Northwest coast, has a history of producing powerful earthquakes. These events highlight the need to understand the region's earthquake probability. This study aims to conduct a sensitivity test on the earthquake probability in the Pacific Northwest, evaluating partial and full rupture scenarios. The study analyzes 32 different earthquake chronologies derived from the earthquake catalog and perturbs them to assess how the probabilities vary with changes in data. As a result, we found that the Southern Oregon and Northern California regions face the highest risk, with a 34-49% chance of a partial rupture and a 28-32% chance of a full rupture within 100 years. Within the next 50 years, probabilities are 17-20% and 13-15%, respectively. The relatively small changes in probabilities suggests that the estimates are robust, indicating that changes in data do not significantly skew the overall probability assessment. These findings emphasize the need to implement hazard mitigation strategies to protect vulnerable Southern Oregon and Northern California communities from future earthquake events.

There are a vast number of pathogens that impact global public health, necessitating an accessible assay capable of detecting multiple targets simultaneously. Lateral flow assays (LFAs) have the potential to fill this role as a cost-effective, rapid, and simple technology instrumental in the detection of many analytes. However, multiplexed detection using nucleic acid LFAs is difficult due to the increased chance of non-specific binding as more targets are added to the assay. In this work, we aim to increase specificity and multiplexing potential in LFAs. We first showcase the process of developing a nucleic acid LFA by evaluating both fluorophores and gold nanoparticles to generate a visible signal. As fluorophores require a fluorescent light source, we moved forward with gold nanoparticles, which have a readout visible to the naked eye. Additionally, we automated the LFA fabrication process using an Echo Liquid Handler. Finally, we assessed methods to convert double-stranded to single-stranded DNA, required for compatibility with LFAs. In the future, we look to optimize signal visibility while increasing multiplexability. This work highlights the potential of multiplexed LFAs as a robust technology capable of significantly improving public health responses and outcomes.

Leigh syndrome (LS) is the most common pediatric mitochondrial disease, manifesting in the first year of life and leading to early death due to a lack of proven therapies. Like other mitochondrial diseases, LS is caused by gene mutations impacting proteins essential for the mitochondrial respiratory chain, including all complexes. Mutations in NDUFS4, a gene that encodes a subunit critical for structure and stability of complex I, have been linked to LS. Mice with the whole-body NDUFS4 KO exhibit major LS symptoms, particularly epilepsy, along with psychomotor deterioration, progressive neurodegeneration and premature lethality (~P60). Our earlier findings showed that mice with Ndufs4 KO specifically in GABAergic interneurons (Gad2-Ndufs4-KO) exhibit the severe epilepsy and sudden death observed in the global KO mice. These mice represent an excellent model of LS epilepsy, isolated from other clinical manifestations of the disease. LS related epilepsy is often very difficult to treat and indicative of poor disease prognosis. Chronic hypoxia therapy (CHT) has previously shown promise in improving survival and reversing neurodegeneration in LS mice. Yet its impact on seizures remains unknown. In this study, we investigated the efficacy of CHT in ameliorating the epileptic phenotype. Mice with LS epilepsy demonstrated a longer lifespan when exposed to  normobaric 11% O2 than normoxia from postnatal day 35 to day 70. Upon return to normoxic conditions, mice kept in chronic hypoxia die within days. In addition, preliminary thermal seizure tests show an increased thermal seizure threshold in hypoxic mice compared to normoxic ones.  Future studies will evaluate CHT impact on spontaneous seizures using video EEG technique. Our study will aid in the development of a novel therapeutic approach for seizures and related death in Leigh syndrome.

Tuberculosis (TB) remains the world’s deadliest infectious disease, claiming over 1.25 million lives annually—surpassing malaria and HIV in mortality. TB’s causative pathogen, Mycobacterium tuberculosis (MTB), continues to spread rapidly due to inadequate access to accurate molecular diagnostic tests. The most commonly used tests include sputum-based and tuberculin skin tests, which require follow-up visits and have suboptimal sensitivity, particularly within certain patient populations. Moreover, these assays cannot identify emerging drug-resistant strains (DR-TB) that have reduced susceptibility to first-line antibiotics. Our aim is to design a diagnostic tool to detect cell-free DNA (cfDNA) in urine and identify the infecting strain to ensure patients receive appropriate antibiotics. To achieve this, we are developing a probe-ligation assay with single-nucleotide specificity. Current implementations are limited by the low specificity of ligase, leading to false positives and an inability to differentiate between mutated MTB strains. We hypothesized that Flap Endonuclease-1 (FEN1) could confer a specificity advantage by integrating a second enzymatic “check” into the process. The protocol involves a ligation reaction with MTB genome-derived targets and two probes, each containing a DNA flap with additional nucleotides. To detect the ligated product, FEN1 must cleave these flaps before the ligase catalyzes the repair of the nick between probes. To experimentally observe this, we carried out several ligation reactions containing FEN1 and ligase with wild-type and mutant targets, followed by PCR or gel electrophoresis to measure ligated product formation. We evaluated the efficiency and precision by analyzing the amplification profiles of WT targets and mutants containing SNPs neighboring the ligation site. Our data about whether FEN1 confers a significant specificity advantage remains inconclusive, but the double enzyme reaction is functional and could be further exploited in future experiments with additional optimization or modifications to enzymes or DNA probes.